October 28, 2020

Bioconductors:

We are pleased to announce Bioconductor 3.12, consisting of 1974 software packages, 398 experiment data packages, 968 annotation packages, and 28 workflows.

There are 125 new software packages, 9 new data experiment packages, 2 new annotation packages, 1 new workflow, 2 online books, and many updates and improvements to existing packages; Bioconductor 3.12 is compatible with R 4.0.3, and is supported on Linux, 32- and 64-bit Windows, and macOS 10.14.6 Mojave or higher. This release will include an updated Bioconductor Amazon Machine Image and Docker containers.

Thank you to everyone for your contribution to Bioconductor

Visit Bioconductor BiocViews for details and downloads.

Contents

• Getting Started with Bioconductor 3.12
• New Software Packages
• New Data Experiment Packages
• New Annotation Packages
• New Workflow
• New Online Books
• NEWS from new and existing software packages
• NEWS from new and existing data experiment packages
• NEWS from new and existing workflows
• Deprecated and Defunct Packages

Getting Started with Bioconductor 3.12

To update to or install Bioconductor 3.12:

1. Install R 4.0.3. Bioconductor 3.12 has been designed expressly for this version of R.

2. Follow the instructions at Installing Bioconductor.

New Software Packages

There are 125 new software packages in this release of Bioconductor.

• ADImpute Single-cell RNA sequencing (scRNA-seq) methods are typically unable to quantify the expression levels of all genes in a cell, creating a need for the computational prediction of missing values (‘dropout imputation’). Most existing dropout imputation methods are limited in the sense that they exclusively use the scRNA-seq dataset at hand and do not exploit external gene-gene relationship information. Here we propose two novel methods: a gene regulatory network-based approach using gene-gene relationships learnt from external data and a baseline approach corresponding to a sample-wide average. ADImpute can implement these novel methods and also combine them with existing imputation methods (currently supported: DrImpute, SAVER). ADImpute can learn the best performing method per gene and combine the results from different methods into an ensemble.

• aggregateBioVar For single cell RNA-seq data collected from more than one subject (e.g. biological sample or technical replicates), this package contains tools to summarize single cell gene expression profiles at the level of subject. A SingleCellExperiment object is taken as input and converted to a list of SummarizedExperiment objects, where each list element corresponds to an assigned cell type. The SummarizedExperiment objects contain aggregate gene-by-subject count matrices and inter-subject column metadata for individual subjects that can be processed using downstream bulk RNA-seq tools.

• AlpsNMR Reads Bruker NMR data directories both zipped and unzipped. It provides automated and efficient signal processing for untargeted NMR metabolomics. It is able to interpolate the samples, detect outliers, exclude regions, normalize, detect peaks, align the spectra, integrate peaks, manage metadata and visualize the spectra. After spectra proccessing, it can apply multivariate analysis on extracted data. Efficient plotting with 1-D data is also available. Basic reading of 1D ACD/Labs exported JDX samples is also available.

• ANCOMBC ANCOMBC is a package for normalizing the microbial absolute abundance data due to unequal sampling fractions across samples, and identifying taxa (e.g. phyla, families, genera, species, etc.) that are differentially abundant with respect to the covariate of interest (e.g. study groups) between two or more groups of multiple samples.

• AnVILBilling AnVILBilling helps monitor AnVIL-related costs in R, using queries to a BigQuery table to which costs are exported daily. Functions are defined to help categorize tasks and associated expenditures, and to visualize and explore expense profiles over time. This package will be expanded to help users estimate costs for specific task sets.

• AnVILPublish Use this package to create or update AnVIL workspaces from resources such as R / Bioconductor packages. The metadata about the package (e.g., select information from the package DESCRIPTION file and from vignette YAML headings) are used to populate the ‘DASHBOARD’. Vignettes are translated to python notebooks ready for evaluation in AnVIL.

• bambu bambu is a R package for multi-sample transcript discovery and quantification using long read RNA-Seq data. You can use bambu after read alignment to obtain expression estimates for known and novel transcripts and genes. The output from bambu can directly be used for visualisation and downstream analysis such as differential gene expression or transcript usage.

• BayesSpace Tools for clustering and enhancing the resolution of spatial gene expression experiments. BayesSpace clusters a low-dimensional representation of the gene expression matrix, incorporating a spatial prior to encourage neighboring spots to cluster together. The method can enhance the resolution of the low-dimensional representation into “sub-spots”, for which features such as gene expression or cell type composition can be imputed.

• BiocIO Implements import() and export() standard generics for importing and exporting biological data formats. import() supports whole-file as well as chunk-wise iterative import. The import() interface optionally provides a standard mechanism for ‘lazy’ access via filter() (on row or element-like components of the file resource), select() (on column-like components of the file resource) and collect(). The import() interface optionally provides transparent access to remote (e.g. via https) as well as local access. Developers can register a file extension, e.g., .loom for dispatch from character-based URIs to specific import() / export() methods based on classes representing file types, e.g., LoomFile().

• biocthis This package expands the usethis package with the goal of helping automate the process of creating R packages for Bioconductor or making them Bioconductor-friendly.

• bluster Wraps common clustering algorithms in an easily extended S4 framework. Backends are implemented for hierarchical, k-means and graph-based clustering. Several utilities are also provided to compare and evaluate clustering results.

• BrainSABER The Allen Institute for Brain Science provides an RNA sequencing (RNA-Seq) data resource for studying transcriptional mechanisms involved in human brain development known as BrainSpan. BrainSABER is an R package that facilitates comparison of user data with the various developmental stages and brain structures found in the BrainSpan atlas by generating dynamic similarity heatmaps for the two data sets. It also provides a self-validating container for user data.

• CellaRepertorium Methods to cluster and analyze high-throughput single cell immune cell repertoires, especially from the 10X Genomics VDJ solution. Contains an R interface to CD-HIT (Li and Godzik 2006). Methods to visualize and analyze paired heavy-light chain data. Tests for specific expansion, as well as omnibus oligoclonality under hypergeometric models.

• cfDNAPro cfDNA fragment size metrics are important features for utilizing liquid biopsy in tumor early detection, diagnosis, therapy personlization and monitoring. Analyzing and visualizing insert size metrics could be time intensive. This package intends to simplify this exploration process, and it offers two sets of functions for data characterization and data visualization.

• ChromSCape ChromSCape - Chromatin landscape profiling for Single Cells - is a ready-to-launch user-friendly Shiny Application for the analysis of single-cell epigenomics datasets (scChIP-seq, scATAC-seq, scCUT&Tag, …) from aligned data to differential analysis & gene set enrichment analysis. It is highly interactive, enables users to save their analysis and covers a wide range of analytical steps: QC, preprocessing, filtering, batch correction, dimensionality reduction, vizualisation, clustering, differential analysis and gene set analysis.

• corral Correspondence analysis (CA) is a matrix factorization method, and is similar to principal components analysis (PCA). Whereas PCA is designed for application to continuous, approximately normally distributed data, CA is appropriate for non-negative, count-based data that are in the same additive scale. The corral package implements CA for dimensionality reduction of a single matrix of single-cell data, as well as a multi-table adaptation of CA that leverages data-optimized scaling to align data generated from different sequencing platforms by projecting into a shared latent space. corral utilizes sparse matrices and a fast implementation of SVD, and can be called directly on Bioconductor objects (e.g., SingleCellExperiment) for easy pipeline integration. The package also includes the option to apply CA-style processing to continuous data (e.g., proteomic TOF intensities) with the Hellinger distance adaptation of CA.

• customCMPdb This package serves as a query interface for important community collections of small molecules, while also allowing users to include custom compound collections.

• CytoTree A trajectory inference toolkit for flow and mass cytometry data. CytoTree is a valuable tool to build a tree-shaped trajectory using flow and mass cytometry data. The application of CytoTree ranges from clustering and dimensionality reduction to trajectory reconstruction and pseudotime estimation. It offers complete analyzing workflow for flow and mass cytometry data.

• dasper The aim of dasper is to detect aberrant splicing events from RNA-seq data. dasper will use as input both junction and coverage data from RNA-seq to calculate the deviation of each splicing event in a patient from a set of user-defined controls. dasper uses an unsupervised outlier detection algorithm to score each splicing event in the patient with an outlier score representing the degree to which that splicing event looks abnormal.

• DegNorm This package performs degradation normalization in bulk RNA-seq data to improve differential expression analysis accuracy.

• densvis Implements the density-preserving modification to t-SNE and UMAP described by Narayan et al. (2020) <doi:10.1101/2020.05.12.077776>. The non-linear dimensionality reduction techniques t-SNE and UMAP enable users to summarise complex high-dimensional sequencing data such as single cell RNAseq using lower dimensional representations. These lower dimensional representations enable the visualisation of discrete transcriptional states, as well as continuous trajectory (for example, in early development). However, these methods focus on the local neighbourhood structure of the data. In some cases, this results in misleading visualisations, where the density of cells in the low-dimensional embedding does not represent the transcriptional heterogeneity of data in the original high-dimensional space. den-SNE and densMAP aim to enable more accurate visual interpretation of high-dimensional datasets by producing lower-dimensional embeddings that accurately represent the heterogeneity of the original high-dimensional space, enabling the identification of homogeneous and heterogeneous cell states. This accuracy is accomplished by including in the optimisation process a term which considers the local density of points in the original high-dimensional space. This can help to create visualisations that are more representative of heterogeneity in the original high-dimensional space.

• escape A bridging R package to facilitate gene set enrichment analysis (GSEA) in the context of single-cell RNA sequencing. Using raw count information, Seurat objects, or SingleCellExperiment format, users can perform and visualize GSEA across individual cells.

• ExperimentSubset Experiment objects such as the SummarizedExperiment or SingleCellExperiment are data containers for one or more matrix-like assays along with the associated row and column data. Often only a subset of the original data is needed for down-stream analysis. For example, filtering out poor quality samples will require excluding some columns before analysis. The ExperimentSubset object is a container to efficiently manage different subsets of the same data without having to make separate objects for each new subset.

• famat Famat is made to collect data about lists of genes and metabolites provided by user, and to visualize it through a Shiny app. Information collected is: - Pathways containing some of the user’s genes and metabolites (obtained using a pathway enrichment analysis). - Direct interactions between user’s elements inside pathways. - Information about elements (their identifiers and descriptions). - Go terms enrichment analysis performed on user’s genes. The Shiny app is composed of: - information about genes, metabolites, and direct interactions between them inside pathways. - an heatmap showing which elements from the list are in pathways (pathways are structured in hierarchies). - hierarchies of enriched go terms using Molecular Function and Biological Process.

• FilterFFPE This package finds and filters artificial chimeric reads specifically generated in next-generation sequencing (NGS) process of formalin-fixed paraffin-embedded (FFPE) tissues. These artificial chimeric reads can lead to a large number of false positive structural variation (SV) calls. The required input is an indexed BAM file of a FFPE sample.

• flowCut Common techinical complications such as clogging can result in spurious events and fluorescence intensity shifting, flowCut is designed to detect and remove technical artifacts from your data by removing segments that show statistical differences from other segments.

• fmrs Provides parameter estimation as well as variable selection in Finite Mixture of Accelerated Failure Time Regression and Finite Mixture of Regression Models. Furthermore, this package provides Ridge Regression and Elastic Net.

• FScanR ‘FScanR’ identifies Programmed Ribosomal Frameshifting (PRF) events from BLASTX homolog sequence alignment between targeted genomic/cDNA/mRNA sequences against the peptide library of the same species or a close relative. The output by BLASTX or diamond BLASTX will be used as input of ‘FScanR’ and should be in a tabular format with 14 columns. For BLASTX, the output parameter should be: -outfmt ‘6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qframe sframe’. For diamond BLASTX, the output parameter should be: -outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qframe qframe.

• GCSFilesystem Mounting a Google Cloud bucket to a local directory. The files in the bucket can be viewed and read as if they are locally stored. For using the package, you need to install GCSDokan on Windows or gcsfuse on Linux and MacOs.

• getDEE2 Digital Expression Explorer 2 (or DEE2 for short) is a repository of processed RNA-seq data in the form of counts. It was designed so that researchers could undertake re-analysis and meta-analysis of published RNA-seq studies quickly and easily. As of April 2020, over 1 million SRA datasets have been processed. This package provides an R interface to access these expression data. More information about the DEE2 project can be found at the project homepage (http://dee2.io) and main publication (https://doi.org/10.1093/gigascience/giz022).

• ggtreeExtra ‘ggtreeExtra’ extends the method for mapping and visualizing associated data on phylogenetic tree using ‘ggtree’. These associated data can be mapped to circular layout, fan layout, or other layout tree built by ‘ggtree’ with the grammar of ‘ggplot2’.

• GSEAmining Gene Set Enrichment Analysis is a very powerful and interesting computational method that allows an easy correlation between differential expressed genes and biological processes. Unfortunately, although it was designed to help researchers to interpret gene expression data it can generate huge amounts of results whose biological meaning can be difficult to interpret. Many available tools rely on the hierarchically structured Gene Ontology (GO) classification to reduce reundandcy in the results. However, due to the popularity of GSEA many more gene set collections, such as those in the Molecular Signatures Database are emerging. Since these collections are not organized as those in GO, their usage for GSEA do not always give a straightforward answer or, in other words, getting all the meaninful information can be challenging with the currently available tools. For these reasons, GSEAmining was born to be an easy tool to create reproducible reports to help researchers make biological sense of GSEA outputs. Given the results of GSEA, GSEAmining clusters the different gene sets collections based on the presence of the same genes in the leadind edge (core) subset. Leading edge subsets are those genes that contribute most to the enrichment score of each collection of genes or gene sets. For this reason, gene sets that participate in similar biological processes should share genes in common and in turn cluster together. After that, GSEAmining is able to identify and represent for each cluster: - The most enriched terms in the names of gene sets (as wordclouds) - The most enriched genes in the leading edge subsets (as bar plots). In each case, positive and negative enrichments are shown in different colors so it is easy to distinguish biological processes or genes that may be of interest in that particular study.

• GSgalgoR A multi-objective optimization algorithm for disease sub-type discovery based on a non-dominated sorting genetic algorithm. The ‘Galgo’ framework combines the advantages of clustering algorithms for grouping heterogeneous ‘omics’ data and the searching properties of genetic algorithms for feature selection. The algorithm search for the optimal number of clusters determination considering the features that maximize the survival difference between sub-types while keeping cluster consistency high.

• GWAS.BAYES This package is built to perform GWAS analysis for selfing species. The research related to this package was supported in part by National Science Foundation Award 1853549.

• GWENA The development of high-throughput sequencing led to increased use of co-expression analysis to go beyong single feature (i.e. gene) focus. We propose GWENA (Gene Whole co-Expression Network Analysis) , a tool designed to perform gene co-expression network analysis and explore the results in a single pipeline. It includes functional enrichment of modules of co-expressed genes, phenotypcal association, topological analysis and comparison of networks configuration between conditions.

• HCAMatrixBrowser The HCAMatrixBrowser queries the HCA matrix endpoint to download expression data and returns a standard Bioconductor object. It uses the LoomExperiment package to serve matrix data that is downloaded as HDF5 loom format.

• Herper Many tools for data analysis are not available in R, but are present in public repositories like conda. The Herper package provides a comprehensive set of functions to interact with the conda package managament system. With Herper users can install, manage and run conda packages from the comfort of their R session. Herper also provides an ad-hoc approach to handling external system requirements for R packages. For people developing packages with python conda dependencies we recommend using basilisk (https://bioconductor.org/packages/release/bioc/html/basilisk.html) to internally support these system requirments pre-hoc.

• HPAStainR This package is built around the HPAStainR function. The purpose of the HPAStainR function is to query the visual staining data in the Human Protein Atlas to return a table of staining ranked cell types. The function also has multiple arguements to personalize to output as well to include cancer data, csv readable names, modify the confidence levels of the results and more. The other functions exist exlcusively to easily acquire the data required to run HPAStainR.

• hummingbird A package for detecting differential methylation. It exploits a Bayesian hidden Markov model that incorporates location dependence among genomic loci, unlike most existing methods that assume independence among observations. Bayesian priors are applied to permit information sharing across an entire chromosome for improved power of detection. The direct output of our software package is the best sequence of methylation states, eliminating the use of a subjective, and most of the time an arbitrary, threshold of p-value for determining significance. At last, our methodology does not require replication in either or both of the two comparison groups.

• idpr ‘idpr’ aims to integrate tools for the computational analysis of intrinsically disordered proteins (IDPs) within R. This package is used to identify known characteristics of IDPs for a sequence of interest with easily reported and dynamic results. Additionally, this package includes tools for IDP-based sequence analysis to be used in conjunction with other R packages.

• ILoReg ILoReg is a tool for identification of cell populations from scRNA-seq data. In particular, ILoReg is useful for finding cell populations with subtle transcriptomic differences. The method utilizes a self-supervised learning method, called Iteratitive Clustering Projection (ICP), to find cluster probabilities, which are used in noise reduction prior to PCA and the subsequent hierarchical clustering and t-SNE steps. Additionally, functions for differential expression analysis to find gene markers for the populations and gene expression visualization are provided.

• infinityFlow Pipeline to analyze and merge data files produced by BioLegend’s LEGENDScreen or BD Human Cell Surface Marker Screening Panel (BD Lyoplates).

• Informeasure This package compiles most information measures currently available: mutual information, conditional mutual information, interaction information, partial information decomposition and part mutual information. Using gene expression profile data, all these estimators can be employed to quantify nonlinear dependence between variables in biological regulatory network inference. The first estimator is used to infer bivariate network while the last four estimators are dedicated to analyze trivariate networks.

• ISAnalytics In gene therapy, stem cells are modified using viral vectors to deliver the therapeutic transgene and replace functional properties since the genetic modification is stable and inherited in all cell progeny. The retrieval and mapping of the sequences flanking the virus-host DNA junctions allows the identification of insertion sites (IS), essential for monitoring the evolution of genetically modified cells in vivo. A comprehensive toolkit for the analysis of IS is required to foster clonal trackign studies and supporting the assessment of safety and long term efficacy in vivo. This package is aimed at (1) supporting automation of IS workflow, (2) performing base and advance analysis for IS tracking (clonal abundance, clonal expansions and statistics for insertional mutagenesis, etc.), (3) providing basic biology insights of transduced stem cells in vivo.

• lefser lefser is an implementation in R of the popular “LDA Effect Size (LEfSe)” method for microbiome biomarker discovery. It uses the Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis to find biomarkers of groups and sub-groups.

• marr marr (Maximum Rank Reproducibility) is a nonparametric approach that detects reproducible signals using a maximal rank statistic for high-dimensional biological data. In this R package, we implement functions that measures the reproducibility of features per sample pair and sample pairs per feature in high-dimensional biological replicate experiments. The user-friendly plot functions in this package also plot histograms of the reproducibility of features per sample pair and sample pairs per feature. Furthermore, our approach also allows the users to select optimal filtering threshold values for the identification of reproducible features and sample pairs based on output visualization checks (histograms).

• megadepth This package provides an R interface to Megadepth by Christopher Wilks available at (https://github.com/ChristopherWilks/megadepth). It is particularly useful for computing the coverage of a set of genomic regions across bigWig or BAM files. With this package, you can build base-pair coverage matrices for regions or annotations of your choice from BigWig files. Megadepth was used to create the raw files provided by https://bioconductor.org/packages/recount3.

• MesKit MesKit provides commonly used analysis and visualization modules based on mutational data generated by multi-region sequencing (MRS). This package allows to decipher ITH, infer metastatic routes as well as uncover the underlying process of mutagenesis. Shiny application was also developed for a need of GUI-based analysis. As a handy tool, MesKit can facilitate the understanding of cancer cell evolution and its relevance to cancer therapeutics.

• metabCombiner This package aligns LC-HRMS metabolomics datasets acquired from biologically similar specimens analyzed under similar, but not necessarily identical, conditions. Two peak-picked and aligned metabolomics feature tables (consisting of m/z, rt, and per-sample abundance measurements, plus optional identifiers & adduct annotations) are accepted as input. The package outputs a combined table of feature pair alignments, organized into groups of similar m/z, and ranked by a similarity score. Input tables are assumed to be acquired using similar (but not necessarily identical) analytical methods.

• metabolomicsWorkbenchR This package provides functions for interfacing with the Metabolomics Workbench RESTful API. Study, compound, protein and gene information can be searched for using the API. Methods to obtain study data in common Bioconductor formats such as SummarizedExperiment and MultiAssayExperiment are also included.

• MethReg Epigenome-wide association studies (EWAS) detects a large number of DNA methylation differences, often hundreds of differentially methylated regions and thousands of CpGs, that are significantly associated with a disease, many are located in non-coding regions. Therefore, there is a critical need to better understand the functional impact of these CpG methylations and to further prioritize the significant changes. MethReg is an R package for integrative modeling of DNA methylation, target gene expression and transcription factor binding sites data, to systematically identify and rank functional CpG methylations. MethReg evaluates, prioritizes and annotates CpG sites with high regulatory potential using matched methylation and gene expression data, along with external TF-target interaction databases based on manually curation, ChIP-seq experiments or gene regulatory network analysis.

• microbiomeExplorer The MicrobiomeExplorer R package is designed to facilitate the analysis and visualization of marker-gene survey feature data. It allows a user to perform and visualize typical microbiome analytical workflows either through the command line or an interactive Shiny application included with the package. In addition to applying common analytical workflows the application enables automated analysis report generation.

• MOFA2 The MOFA2 package contains a collection of tools for running and analysing MOFA models.

• MOGAMUN MOGAMUN is a multi-objective genetic algorithm that identifies active modules in a multiplex biological network. This allows analyzing different biological networks at the same time. MOGAMUN is based on NSGA-II (Non-Dominated Sorting Genetic Algorithm, version II), which we adapted to work on networks.

• MouseFM This package provides methods for genetic finemapping in inbred mice by taking advantage of their very high homozygosity rate (>95%).

• MSEADbi Interface to construct annotation package for MSEA (MSEA.XXX.pb.db). The program design is same as Bioconductor LRBaseDbi or MeSHDbi pacakge, and the usage is also the same as these packages.

• msImpute MsImpute is a package for imputation of peptide intensity in proteomics experiments. It additionally contains tools for MAR/MNAR diagnosis and assessment of distortions to the probability distribution of the data post imputation. Currently, msImpute completes missing values by low-rank approximation of the underlying data matrix.

• MSPrep Package performs summarization of replicates, filtering by frequency, several different options for imputing missing data, and a variety of options for transforming, batch correcting, and normalizing data.

• MSstatsConvert MSstatsConvert provides tools for importing reports of Mass Spectrometry data processing tools into R format suitable for statistical analysis using the MSstats and MSstatsTMT packages.

• MSstatsPTM MSstatsPTM provides general statistical methods for quantitative characterization of post-translational modifications (PTMs). Typically, the analysis involves the quantification of PTM sites (i.e., modified residues) and their corresponding proteins, as well as the integration of the quantification results. MSstatsPTM provides functions for summarization, estimation of PTM site abundance, and detection of changes in PTMs across experimental conditions.

• MSstatsTMTPTM Tools for Post Translational Modification (PTM) and protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling. The functions in this package should be used after PTM/protein summarization. They can be used to both plot the summarized results and model the summarized datasets.

• MultiBaC MultiBaC is a strategy to correct batch effects from multiomic datasets distributed across different labs or data acquisition events. MultiBaC is the first Batch effect correction algorithm that dealing with batch effect correction in multiomics datasets. MultiBaC is able to remove batch effects across different omics generated within separate batches provided that at least one common omic data type is included in all the batches considered.

• multicrispr This package is for designing Crispr/Cas9 and Prime Editing experiments. It contains functions to (1) define and transform genomic targets, (2) find spacers (4) count offtarget (mis)matches, and (5) compute Doench2016/2014 targeting efficiency. Care has been taken for multicrispr to scale well towards large target sets, enabling the design of large Crispr/Cas9 libraries.

• multiGSEA Extracted features from pathways derived from 8 different databases (KEGG, Reactome, Biocarta, etc.) can be used on transcriptomic, proteomic, and/or metabolomic level to calculate a combined GSEA-based enrichment score.

• musicatk Mutational signatures are carcinogenic exposures or aberrant cellular processes that can cause alterations to the genome. We created musicatk (MUtational SIgnature Comprehensive Analysis ToolKit) to address shortcomings in versatility and ease of use in other pre-existing computational tools. Although many different types of mutational data have been generated, current software packages do not have a flexible framework to allow users to mix and match different types of mutations in the mutational signature inference process. Musicatk enables users to count and combine multiple mutation types, including SBS, DBS, and indels. Musicatk calculates replication strand, transcription strand and combinations of these features along with discovery from unique and proprietary genomic feature associated with any mutation type. Musicatk also implements several methods for discovery of new signatures as well as methods to infer exposure given an existing set of signatures. Musicatk provides functions for visualization and downstream exploratory analysis including the ability to compare signatures between cohorts and find matching signatures in COSMIC V2 or COSMIC V3.

• NanoMethViz NanoMethViz is a toolkit for visualising methylation data from Oxford Nanopore sequencing. It can be used to explore methylation patterns from reads derived from Oxford Nanopore direct DNA sequencing with methylation called by callers including nanopolish, f5c and megalodon. The plots in this package allow the visualisation of methylation profiles aggregated over experimental groups and across classes of genomic features.

• ncRNAtools ncRNAtools provides a set of basic tools for handling and analyzing non-coding RNAs. These include tools to access the RNAcentral database and to predict and visualize the secondary structure of non-coding RNAs. The package also provides tools to read, write and interconvert the file formats most commonly used for representing such secondary structures.

• nearBynding Provides a pipeline to discern RNA structure at and proximal to the site of protein binding within regions of the transcriptome defined by the user. CLIP protein-binding data can be input as either aligned BAM or peak-called bedGraph files. RNA structure can either be predicted internally from sequence or users have the option to input their own RNA structure data. RNA structure binding profiles can be visually and quantitatively compared across multiple formats.

• Nebulosa This package provides a enhanced visualization of single-cell data based on gene-weighted density estimation. Nebulosa recovers the signal from dropped-out features and allows the inspection of the joint expression from multiple features (e.g. genes). Seurat and SingleCellExperiment objects can be used within Nebulosa.

• NewWave A model designed for dimensionality reduction and batch effect removal for scRNA-seq data. It is designed to be massively parallelizable using shared objects that prevent memory duplication, and it can be used with different mini-batch approaches in order to reduce time consumption. It assumes a negative binomial distribution for the data with a dispersion parameter that can be both commonwise across gene both genewise.

• Omixer Omixer - an R package for multivariate and reproducible randomization with lab-friendly sample layouts. Omixer ensures optimal sample distribution across batches with well-documented methods, and can output intuitive sample sheets for the wet lab if needed.

• padma Use multiple factor analysis to calculate individualized pathway-centric scores of deviation with respect to the sampled population based on multi-omic assays (e.g., RNA-seq, copy number alterations, methylation, etc). Graphical and numerical outputs are provided to identify highly aberrant individuals for a particular pathway of interest, as well as the gene and omics drivers of aberrant multi-omic profiles.

• pageRank Implemented temporal PageRank analysis as defined by Rozenshtein and Gionis. Implemented multiplex PageRank as defined by Halu et al. Applied temporal and multiplex PageRank in gene regulatory network analysis.

• PeacoQC This is a package that includes pre-processing and quality control functions that can remove margin events, compensate and transform the data and that will use PeacoQCSignalStability for quality control. This last function will first detect peaks in each channel of the flowframe. It will remove anomalies based on the IsolationTree function and the MAD outlier detection method. This package can be used for both flow- and mass cytometry data.

• periodicDNA This R package helps the user identify k-mers (e.g. di- or tri-nucleotides) present periodically in a set of genomic loci (typically regulatory elements). The functions of this package provide a straightforward approach to find periodic occurrences of k-mers in DNA sequences, such as regulatory elements. It is not aimed at identifying motifs separated by a conserved distance; for this type of analysis, please visit MEME website.

• PhosR PhosR is a package for the comprenhensive analysis of phosphoproteomic data. There are two major components to PhosR: processing and downstream analysis. PhosR consists of various processing tools for phosphoproteomics data including filtering, imputation, normalisation, and functional analysis for inferring active kinases and signalling pathways.

• pipeComp A simple framework to facilitate the comparison of pipelines involving various steps and parameters. The pipelineDefinition class represents pipelines as, minimally, a set of functions consecutively executed on the output of the previous one, and optionally accompanied by step-wise evaluation and aggregation functions. Given such an object, a set of alternative parameters/methods, and benchmark datasets, the runPipeline function then proceeds through all combinations arguments, avoiding recomputing the same step twice and compiling evaluations on the fly to avoid storing potentially large intermediate data.

• POMA POMA introduces a structured, reproducible and easy-to-use workflow for the visualization, pre-processing, exploratory and statistical analysis of mass spectrometry data. The main aim of POMA is to enable a flexible data cleaning and statistical analysis processes in one comprehensible and user-friendly R package. This package also has a Shiny app version that implements all POMA functions. See https://github.com/pcastellanoescuder/POMAShiny.

• preciseTAD preciseTAD provides functions to predict the location of boundaries of topologically associated domains (TADs) and chromatin loops at base-level resolution. As an input, it takes BED-formatted genomic coordinates of domain boundaries detected from low-resolution Hi-C data, and coordinates of high-resolution genomic annotations from ENCODE or other consortia. preciseTAD employs several feature engineering strategies and resampling techniques to address class imbalance, and trains an optimized random forest model for predicting low-resolution domain boundaries. Translated on a base-level, preciseTAD predicts the probability for each base to be a boundary. Density-based clustering and scalable partitioning techniques are used to detect precise boundary regions and summit points. Compared with low-resolution boundaries, preciseTAD boundaries are highly enriched for CTCF, RAD21, SMC3, and ZNF143 signal and more conserved across cell lines. The pre-trained model can accurately predict boundaries in another cell line using CTCF, RAD21, SMC3, and ZNF143 annotation data for this cell line.

• proActiv Most human genes have multiple promoters that control the expression of different isoforms. The use of these alternative promoters enables the regulation of isoform expression pre-transcriptionally. Alternative promoters have been found to be important in a wide number of cell types and diseases. proActiv is an R package that enables the analysis of promoters from RNA-seq data. proActiv uses aligned reads as input, and generates counts and normalized promoter activity estimates for each annotated promoter. In particular, proActiv accepts junction files from TopHat2 or STAR or BAM files as inputs. These estimates can then be used to identify which promoter is active, which promoter is inactive, and which promoters change their activity across conditions.

• QFeatures The QFeatures infrastructure enables the management and processing of quantitative features for high-throughput mass spectrometry assays. It provides a familiar Bioconductor user experience to manages quantitative data across different assay levels (such as peptide spectrum matches, peptides and proteins) in a coherent and tractable format.

• RadioGx Computational tool box for radio-genomic analysis which integrates radio-response data, radio-biological modelling and comprehensive cell line annotations for hundreds of cancer cell lines. The ‘RadioSet’ class enables creation and manipulation of standardized datasets including information about cancer cells lines, radio-response assays and dose-response indicators. Included methods allow fitting and plotting dose-response data using established radio-biological models along with quality control to validate results. Additional functions related to fitting and plotting dose response curves, quantifying statistical correlation and calculating area under the curve (AUC) or survival fraction (SF) are included. For more details please see the included documentation, references, as well as: Manem, V. et al (2018) <doi:10.1101/449793>.

• rebook Provides utilities to re-use content across chapters of a Bioconductor book. This is mostly based on functionality developed while writing the OSCA book, but generalized for potential use in other large books with heavy compute. Also contains some functions to assist book deployment.

• recount3 Explore and download data from the recount project available at https://jhubiostatistics.shinyapps.io/recount3/. Using the recount3 package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression analysis. Using data from the recount3 project you can perform annotation-agnostic differential expression analyses as described at http://doi.org/TODO.

• recountmethylation Access cross-study compilations of DNA methylation array databases. Database files can be downloaded and accessed using provided functions. Background about database file types (HDF5 and HDF5-SummarizedExperiment), SummarizedExperiment classes, and examples for data handling, validation, and analyses, can be found in the package vignettes. Note the disclaimer on package load, and consult the main manuscript for further info.

• RegEnrich This package is a pipeline to identify the key gene regulators in a biological process, for example in cell differentiation and in cell development after stimulation. There are four major steps in this pipeline: (1) differential expression analysis; (2) regulator-target network inference; (3) enrichment analysis; and (4) regulators scoring and ranking.

• ResidualMatrix Provides delayed computation of a matrix of residuals after fitting a linear model to each column of an input matrix. Also supports partial computation of residuals where selected factors are to be preserved in the output matrix. Implements a number of efficient methods for operating on the delayed matrix of residuals, most notably matrix multiplication and calculation of row/column sums or means.

• Rfastp Rfastp is an R wrapper of fastp developed in c++. fastp performs quality control for fastq files. including low quality bases trimming, polyX trimming, adapter auto-detection and trimming, paired-end reads merging, UMI sequence/id handling. Rfastp can concatenate multiple files into one file (like shell command cat) and accept multiple files as input.

• RIPAT RIPAT is developed as an R package for retroviral integration sites annotation and distribution analysis. RIPAT needs local alignment results from BLAST and BLAT. Specific input format is depicted in RIPAT manual. RIPAT provides RV integration pattern analysis result as forms of R objects, excel file with multiple sheets and plots.

• rnaEditr RNAeditr analyzes site-specific RNA editing events, as well as hyper-editing regions. The editing frequencies can be tested against binary, continuous or survival outcomes. Multiple covariate variables as well as interaction effects can also be incorporated in the statistical models.

• RnaSeqSampleSize RnaSeqSampleSize package provides a sample size calculation method based on negative binomial model and the exact test for assessing differential expression analysis of RNA-seq data. It controls FDR for multiple testing and utilizes the average read count and dispersion distributions from real data to estimate a more reliable sample size. It is also equipped with several unique features, including estimation for interested genes or pathway, power curve visualization, and parameter optimization.

• rsemmed A programmatic interface to the Semantic MEDLINE database. It provides functions for searching the database for concepts and finding paths between concepts. Path searching can also be tailored to user specifications, such as placing restrictions on concept types and the type of link between concepts. It also provides functions for summarizing and visualizing those paths.

• Rtpca R package for performing thermal proximity co-aggregation analysis with thermal proteome profiling datasets to analyse protein complex assembly and (differential) protein-protein interactions across conditions.

• sangeranalyseR This package builds on sangerseqR to allow users to create contigs from collections of Sanger sequencing reads. It provides a wide range of options for a number of commonly-performed actions including read trimming, detecting secondary peaks, and detecting indels using a reference sequence. All parameters can be adjusted interactively either in R or in the associated Shiny applications. There is extensive online documentation, and the package can outputs detailed HTML reports, including chromatograms.

• SCATE SCATE is a software tool for extracting and enhancing the sparse and discrete Single-cell ATAC-seq Signal. Single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) is the state-of-the-art technology for analyzing genome-wide regulatory landscapes in single cells. Single-cell ATAC-seq data are sparse and noisy, and analyzing such data is challenging. Existing computational methods cannot accurately reconstruct activities of individual cis-regulatory elements (CREs) in individual cells or rare cell subpopulations. SCATE was developed to adaptively integrate information from co-activated CREs, similar cells, and publicly available regulome data and substantially increase the accuracy for estimating activities of individual CREs. We demonstrate that SCATE can be used to better reconstruct the regulatory landscape of a heterogeneous sample.

• scCB2 scCB2 is an R package implementing CB2 for distinguishing real cells from empty droplets in droplet-based single cell RNA-seq experiments (especially for 10x Chromium). It is based on clustering similar barcodes and calculating Monte-Carlo p-value for each cluster to test against background distribution. This cluster-level test outperforms single-barcode-level tests in dealing with low count barcodes and homogeneous sequencing library, while keeping FDR well controlled.

• scDataviz In the single cell World, which includes flow cytometry, mass cytometry, single-cell RNA-seq (scRNA-seq), and others, there is a need to improve data visualisation and to bring analysis capabilities to researchers even from non-technical backgrounds. scDataviz attempts to fit into this space, while also catering for advanced users. Additonally, due to the way that scDataviz is designed, which is based on SingleCellExperiment, it has a ‘plug and play’ feel, and immediately lends itself as flexibile and compatibile with studies that go beyond scDataviz. Finally, the graphics in scDataviz are generated via the ggplot engine, which means that users can ‘add on’ features to these with ease.

• SCFA Subtyping via Consensus Factor Analysis (SCFA) can efficiently remove noisy signals from consistent molecular patterns in multi-omics data. SCFA first uses an autoencoder to select only important features and then repeatedly performs factor analysis to represent the data with different numbers of factors. Using these representations, it can reliably identify cancer subtypes and accurately predict risk scores of patients.

• scp Utility functions for manipulating, processing, and analyzing mass spectrometry-based single-cell proteomics (SCP) data. The package is an extension to the ‘QFeatures’ package designed for SCP applications.

• scRepertoire scRepertoire was built to process data derived from the 10x Genomics Chromium Immune Profiling for both T-cell receptor (TCR) and immunoglobulin (Ig) enrichment workflows and subsequently interacts with the popular Seurat and SingleCellExperiment R packages.

• scuttle Provides basic utility functions for performing single-cell analyses, focusing on simple normalization, quality control and data transformations. Also provides some helper functions to assist development of other packages.

• SeqGate Filtering of lowly expressed features (e.g. genes) is a common step before performing statistical analysis, but an arbitrary threshold is generally chosen. SeqGate implements a method that rationalize this step by the analysis of the distibution of counts in replicate samples. The gate is the threshold above which sequenced features can be considered as confidently quantified.

• simplifyEnrichment A new method (binary cut) is proposed to effectively cluster GO terms into groups from the semantic similarity matrix. Summaries of GO terms in each cluster are visualized by word clouds.

• snifter Provides an R wrapper for the implementation of FI-tSNE from the python package openTNSE. See Poličar et al. (2019) <doi:10.1101/731877> and the algorithm described by Linderman et al. (2018) <doi:10.1038/s41592-018-0308-4>.

• SpatialDecon Using spatial or bulk gene expression data, estimates abundance of mixed cell types within each observation. Based on “Advances in mixed cell deconvolution enable quantification of cell types in spatially-resolved gene expression data”, Danaher (2020). Designed for use with the NanoString GeoMx platform, but applicable to any gene expression data.

• SpatialExperiment Defines S4 classes for storing data for spatial experiments. Main examples are reported by using seqFISH and 10x-Visium Spatial Gene Expression data. This includes specialized methods for storing, retrieving spatial coordinates, 10x dedicated parameters and their handling.

• spatialHeatmap The spatialHeatmap package provides functionalities for visualizing cell-, tissue- and organ-specific data of biological assays by coloring the corresponding spatial features defined in anatomical images according to a numeric color key.

• Spectra The Spectra package defines an efficient infrastructure for storing and handling mass spectrometry spectra and functionality to subset, process, visualize and compare spectra data. It provides different implementations (backends) to store mass spectrometry data. These comprise backends tuned for fast data access and processing and backends for very large data sets ensuring a small memory footprint.

• SPsimSeq SPsimSeq uses a specially designed exponential family for density estimation to constructs the distribution of gene expression levels from a given real RNA sequencing data (single-cell or bulk), and subsequently simulates a new dataset from the estimated marginal distributions using Gaussian-copulas to retain the dependence between genes. It allows simulation of multiple groups and batches with any required sample size and library size.

• systemPipeShiny systemPipeShiny (SPS) extends the widely used systemPipeR (SPR) workflow environment with a versatile graphical user interface provided by a Shiny App. This allows non-R users, such as experimentalists, to run many systemPipeR’s workflow designs, control, and visualization functionalities interactively without requiring knowledge of R. Most importantly, SPS has been designed as a general purpose framework for interacting with other R packages in an intuitive manner. Like most Shiny Apps, SPS can be used on both local computers as well as centralized server-based deployments that can be accessed remotely as a public web service for using SPR’s functionalities with community and/or private data. The framework can integrate many core packages from the R/Bioconductor ecosystem. Examples of SPS’ current functionalities include: (a) interactive creation of experimental designs and metadata using an easy to use tabular editor or file uploader; (b) visualization of workflow topologies combined with auto-generation of R Markdown preview for interactively designed workflows; (d) access to a wide range of data processing routines; (e) and an extendable set of visualization functionalities. Complex visual results can be managed on a ‘Canvas Workbench’ allowing users to organize and to compare plots in an efficient manner combined with a session snapshot feature to continue work at a later time. The present suite of pre-configured visualization examples. The modular design of SPR makes it easy to design custom functions without any knowledge of Shiny, as well as extending the environment in the future with contributions from the community.

• TADCompare TADCompare is an R package designed to identify and characterize differential Topologically Associated Domains (TADs) between multiple Hi-C contact matrices. It contains functions for finding differential TADs between two datasets, finding differential TADs over time and identifying consensus TADs across multiple matrices. It takes all of the main types of HiC input and returns simple, comprehensive, easy to analyze results.

• tidySingleCellExperiment tidySingleCellExperiment is an adapter that abstracts the ‘SingleCellExperiment’ container in the form of tibble and allows the data manipulation, plotting and nesting using ‘tidyverse’

• tidySummarizedExperiment tidySummarizedExperiment is an adapter that abstracts the ‘SingleCellExperiment’ container in the form of tibble and allows the data manipulation, plotting and nesting using ‘tidyverse’

• TileDBArray Implements a DelayedArray backend for reading and writing dense or sparse arrays in the TileDB format. The resulting TileDBArrays are compatible with all Bioconductor pipelines that can accept DelayedArray instances.

• TimiRGeN TimiRGeN (Time Incorporated miR-mRNA Generation of Networks) is a novel R package which functionally analyses and integrates time course miRNA-mRNA differential expression data. This tool can generate small networks within R or export results into cytoscape or pathvisio for more detailed network construction and hypothesis generation. This tool is created for researchers that wish to dive deep into time series multi-omic datasets. TimiRGeN goes further than many other tools in terms of data reduction. Here, potentially hundreds of thousands of potential miRNA-mRNA interactions can be whittled down into a handful of high confidence miRNA-mRNA interactions effecting a signalling pathway, across a time course.

• tomoda This package provides many easy-to-use methods to analyze and visualize tomo-seq data. The tomo-seq technique is based on cryosectioning of tissue and performing RNA-seq on consecutive sections. (Reference: Kruse F, Junker JP, van Oudenaarden A, Bakkers J. Tomo-seq: A method to obtain genome-wide expression data with spatial resolution. Methods Cell Biol. 2016;135:299-307. doi:10.1016/bs.mcb.2016.01.006) The main purpose of the package is to find zones with similar transcriptional profiles and spatially expressed genes in a tomo-seq sample. Several visulization functions are available to create easy-to-modify plots.

• ToxicoGx Contains a set of functions to perform large-scale analysis of toxicogenomic data, providing a standardized data structure to hold information relevant to annotation, visualization and statistical analysis of toxicogenomic data.

• transomics2cytoscape transomics2cytoscape generates a file for 3D transomics visualization by providing input that specifies the IDs of multiple KEGG pathway layers, their corresponding Z-axis heights, and an input that represents the edges between the pathway layers. The edges are used, for example, to describe the relationships between kinase on a pathway and enzyme on another pathway. This package automates creation of a transomics network as shown in the figure in Yugi.2014 (https://doi.org/10.1016/j.celrep.2014.07.021) using Cytoscape automation (https://doi.org/10.1186/s13059-019-1758-4).

• UMI4Cats UMI-4C is a technique that allows characterization of 3D chromatin interactions with a bait of interest, taking advantage of a sonication step to produce unique molecular identifiers (UMIs) that help remove duplication bias, thus allowing a better differential comparsion of chromatin interactions between conditions. This package allows processing of UMI-4C data, starting from FastQ files provided by the sequencing facility. It provides two statistical methods for detecting differential contacts and includes a visualization function to plot integrated information from a UMI-4C assay.

• uncoverappLib a Shiny application containing a suite of graphical and statistical tools to support clinical assessment of low coverage regions.It displays three web pages each providing a different analysis module: Coverage analysis, calculate AF by allele frequency app and binomial distribution.

• velociraptor This package provides Bioconductor-friendly wrappers for RNA velocity calculations in single-cell RNA-seq data. We use the basilisk package to manage Conda environments, and the zellkonverter package to convert data structures between SingleCellExperiment (R) and AnnData (Python). The information produced by the velocity methods is stored in the various components of the SingleCellExperiment class.

• VERSO Mutations that rapidly accumulate in viral genomes during a pandemic can be used to track the evolution of the virus and, accordingly, unravel the viral infection network. To this extent, sequencing samples of the virus can be employed to estimate models from genomic epidemiology and may serve, for instance, to estimate the proportion of undetected infected people by uncovering cryptic transmissions, as well as to predict likely trends in the number of infected, hospitalized, dead and recovered people. VERSO is an algorithmic framework that processes variants profiles from viral samples to produce phylogenetic models of viral evolution. The approach solves a Boolean Matrix Factorization problem with phylogenetic constraints, by maximizing a log-likelihood function. VERSO includes two separate and subsequent steps; in this package we provide an R implementation of VERSO STEP 1.

• VplotR The pattern of digestion and protection from DNA nucleases such as DNAse I, micrococcal nuclease, and Tn5 transposase can be used to infer the location of associated proteins. This package contains useful functions to analyze patterns of paired-end sequencing fragment density. VplotR facilitates the generation of V-plots and footprint profiles over single or aggregated genomic loci of interest.

• wpm This is a shiny application for creating well-plate plans. It uses a backtracking-inspired algorithm to place samples on plates based on specific neighborhood constraints.

• zellkonverter Provides methods to convert between Python AnnData objects and SingleCellExperiment objects. These are primarily intended for use by downstream Bioconductor packages that wrap Python methods for single-cell data analysis. It also includes functions to read and write H5AD files used for saving AnnData objects to disk.

New Data Experiment Packages

There are 9 new data experiment packages in this release of Bioconductor.

• celldex Provides a collection of reference expression datasets with curated cell type labels, for use in procedures like automated annotation of single-cell data or deconvolution of bulk RNA-seq.

• clustifyrdatahub References made from external single-cell mRNA sequencing data sets, stored as average gene expression matrices. For use with clustifyr https://bioconductor.org/packages/clustifyr to assign cell type identities.

• DropletTestFiles Assorted files generated from droplet-based single-cell protocols, to be used for testing functions in DropletUtils. Primarily intended for storing files that directly come out of processing pipelines like 10X Genomics’ CellRanger software, prior to the formation of a SingleCellExperiment object. Unlike other packages, this is not designed to provide objects that are immediately ready for analysis.

• FieldEffectCrc Processed RNA-seq data for 1,139 human primary colorectal tissue samples across three phenotypes, including tumor, normal adjacent-to-tumor, and healthy, available as Synapse ID syn22237139 on synapse.org. Data have been parsed into SummarizedExperiment objects available via ExperimentHub to facilitate reproducibility and extension of results from Dampier et al. (PMCID: PMC7386360, PMID: 32764205).

• MethylSeqData Base-level (i.e. cytosine-level) counts for a collection of public bisulfite-seq datasets (e.g., WGBS and RRBS), provided as SummarizedExperiment objects with sample- and base-level metadata.

• NanoporeRNASeq The NanoporeRNASeq package contains long read RNA-Seq data generated using Oxford Nanopore Sequencing. The data consists of 6 samples from two human cell lines (K562 and MCF7) that were generated by the SG-NEx project. Each of these cell lines has three replicates, with 1 direct RNA sequencing data and 2 cDNA sequencing data. Reads are aligned to chromosome 22 (Grch38) and stored as bam files. The original data is from the SG-NEx project.

• SCATEData SCATEData is an ExperimentHub package for SCATE which is a software tool for extracting and enhancing the sparse and discrete Single-cell ATAC-seq Signal.

• timecoursedata This data package contains timecourse gene expression data sets. The first dataset, from Shoemaker et al, consists of microarray samples from lung tissue of mice exposed to different influenzy strains from 14 timepoints. The two other datasets are leaf and root samples from sorghum crops exposed to pre- and post-flowering drought stress and a control condition, sampled across the plants lifetime.

• TMExplorer This package provides a tool to search and download a collection of tumour microenvironment single-cell RNA sequencing datasets and their metadata. TMExplorer aims to act as a single point of entry for users looking to study the tumour microenvironment at the single cell level. Users can quickly search available datasets using the metadata table and then download the ones they are interested in for analysis.

New Annotation Packages

There are two new annotation packages in this release of Bioconductor.

• metaboliteIDmapping The package provides a comprehensive mapping table of nine different Metabolite ID formats and their common name. The data has been collected and merged from four publicly available source, including HMDB, Comptox Dashboard, ChEBI, and the graphite Bioconductor R package.

• geneplast.data The package geneplast.data provides an interface for obtaining input data used in the analyses pipelines from geneplast package. Objects containing species, phylogenetic trees, and orthology information of eukaryotes from different orthologous databases are provided

New Workflow Packages

There is 1 new workflow package in this release of Bioconductor.

• BP4RNAseq An automated pipe for reproducible RNA-seq analysis with the minimal efforts from researchers. The package can process bulk RNA-seq data and single-cell RNA-seq data. You can only provide the taxa name and the accession id of RNA-seq data deposited in the National Center for Biotechnology Information (NCBI). After a cup of tea or longer, you will get formated gene expression data as gene count and transcript count based on both alignment-based and alignment-free workflows.

New Online Books

There are 2 online books in this release of Bioconductor. While the OSCA book has been around for a longer period of time than this release, this is the first release where the book is being hosted, built. and checked by the Bioconductor builders.

• OSCA This is the website for “Orchestrating Single-Cell Analysis with Bioconductor”, a book that teaches users some common workflows for the analysis of single-cell RNA-seq data (scRNA-seq). This book will teach you how to make use of cutting-edge Bioconductor tools to process, analyze, visualize, and explore scRNA-seq data. Additionally, it serves as an online companion for the manuscript “Orchestrating Single-Cell Analysis with Bioconductor”.

• SingleRBook This book covers the use of SingleR, one implementation of an automated annotation method. If you want a survey of different annotation methods - this book is not for you. If you want to create hand-crafted cluster definitions - this book is not for you. (Read the other one instead.) If you want to use the pre-Bioconductor version of the package - this book is not for you. But if you’re tired of manually annotating your single-cell data and you want to do something better with your life, then read on.

NEWS from new and existing Software Packages

a4

                   Changes in version 1.37.2                        

• add imports utils packageDescription

a4Base

                   Changes in version 1.37.3                        

• fix specification of link for fct with different name help page

                   Changes in version 1.37.2                        
  

• use Imports rather than Depends + use roxygen2 for documentation

• use Authors@R

• replace toptable (deprecated in limma 3.36.0) by limma:::.topTableT

                   Changes in version 1.37.1                        
  

• spectralMap: fix legend win-32

a4Classif

                   Changes in version 1.37.1                        

• use Imports rather than Depends + use roxygen2 for documentation

• use Authors@R

• add vignette, examples

a4Core

                   Changes in version 1.37.1                        

• use Imports rather than Depends + use roxygen2 for documentation

• use Authors@R

• add vignette

a4Preproc

                   Changes in version 1.37.1                        

• use Imports rather than Depends + use roxygen2 for documentation

• use Authors@R

• add vignette

a4Reporting

                   Changes in version 1.37.1                        

• use Imports rather than Depends + use roxygen2 for documentation

• use Authors@R

• add vignette

ADImpute

                    Changes in version 2.1.0                        

• Added a NEWS.md file to track changes to the package.

AffiXcan

                    Changes in version 1.7.1                        

BUG FIXED

• Null eigenvectors for TBA with null variance or NA values in the training set are returned correctly

aggregateBioVar

             Changes in version 0.99.0 (2020-09-03)                 

• Submitted to Bioconductor

alevinQC

                    Changes in version 1.5.2                        

• Added selected summary distributions to the reports, and a function to plot histograms of arbitrary numeric columns of the cbTable

AlphaBeta

             Changes in version 1.2.3 (2020-06-06)                  

• Fixed bugs.

• Compatible with new version of dplyr,data.tables

             Changes in version 1.2.1 (2020-04-20)                  
  

• Fixed bugs.

• Made the following significant changes
  • Using ape package to make tree.
  • Added some plots.

• Added SOMA functions.

• Plotting estimates

AlpsNMR

             Changes in version 2.99.5 (2020-10-14)                 

• Bug in bp_kfold_VIP_analysis solved
• Several packages moved from import to depends
• Reexport of some functions removed
• to_rDolphin_blood code reorganized
• Typos removed from tutorial

• norm_pqn_diagnostic$norm_factor used in tutorial instead of plot it

             Changes in version 2.99.4 (2020-09-28)                 
  

• Warning in plot_interactive function added

• Suppressed other warnings of plot_interactive function

             Changes in version 2.99.3 (2020-09-21)                 
  

• sapply calls changed for vapply
• Bioconductor installation instructions included
• MIT license removed
• LazyData: TRUE removed
• Excessive print statements removed from vignettes
• sessionInfo() added to end of vignettes
• Created inst/script directoy to describe inst/extdata source and creation #TODO falta rellenar el archivo

• Commented out code removed

             Changes in version 2.99.2 (2020-08-26)                 
  

• AlpsNMR.Rproj removed from git repository
• Reduced demo dataset to avoid package size > 5 MB

• Modified introduction to alpsnmr vignette and some tests to work with reduced demo dataset

             Changes in version 2.99.1 (2020-08-25)                 
  

• AlpsNMR.Rproj added to gitignore

• Modified examples to avoid create files in main package folder

             Changes in version 2.99.0 (2020-08-24)                 
  

• Added bootstrap and permutation method and some plots related to it

• Minor modifications for bioconductor submision

            Changes in version 2.5.9002 (2020-05-25)                
  

• Changes to pass BiocCheck

• Added permutation test and permutation test plot to nmr_data_analysis

            Changes in version 2.4.9002 (2020-05-13)                
  

• Changes to pass checks for R4

                 Changes in version 2.3.3.9002                      
  

• NIHS_specific removed
• Tests coverage up to 30%
• Update of save_profiling_plots
• Add tutorial
• Remotes installation

• nmr_diagnose is deprecated. Since nmr_diagnose was only used for getting extra normalization information, it was been replaced with nmr_normalize_extra_info that offers a less confusing name.

                 Changes in version 2.3.3.9001                      
  

• Add nmr_identify_regions_cell function
• Add documentation of HMDB_cell
• Vignettes updated
• New functions to apply multilevel statistics

• Update of README file

                    Changes in version 2.3.3                        
  

• Change of nmr_identify_regions_blood function
• Add nmr_identify_regions_urine function
• Add documentation of HMDB_urine
• Add computes_peak_width_ppmfunction for nmr_integrate_peak_positions
• New get_integration_with_metadata
• Vignettes updated

• New functions to apply machine learning to proccessed datasets

                    Changes in version 2.3.2                        
  

• Inclusion of baseline removal using assymetric least squares
• Change the baselineThresh to NULL so it is autodetected
• Vignettes updated including baseline removal
• Bug correction in nmr_baseline_threshold
• Elimination of package vignettes (there is an error to be solved there)
• New nmr_identify_regions function
• Add documentation of HMDB_blood

• New files_to_rDolphin function

                 Changes in version 2.3.1.9000                      
  

• Rename package from NIHSnmr to AlpsNMR

                    Changes in version 2.3.1                        
  

• Change SNR.Th value from 3 to 4 in pipeline_example.R
• Update installation instructions

• Last version form Sergio (changes not significant since 2.3.0)

                    Changes in version 2.3.0                        
  

• Improve installation instructions under R<3.5
• nmr_peak_detection_tune_snr function added.

• Minor bug fixes

                    Changes in version 2.2.0                        
  

• Improve installation instructions
• Clarify Add metadata vignette
• Add normalization diagnostics
• Add some data analysis helpers
• Enable parallellization for sample loading, peak detection and data analysis helpers
• Do not set negative area values to zero, to avoid biasing variances
• Add metadata from a single tidy excel function
• Add nmr_diagnose to get and set diagnostic information
• Add nmr_diagnose support to nmr_normalize

• Minor bug fixes

                    Changes in version 2.1.0                        
  

• Documentation improvements

• nmr_dataset_peak_table object for peak detection results

                    Changes in version 2.0.0                        
  

• Too many changes to be listed here. Check the vignette for a summary of all the features. Use browseVignettes(“NIHSnmr”).

                    Changes in version 1.2.0                        
  

Breaking changes

• Rename injection_id to NMRExperiment.

• nmr_dataset_load and nmr_dataset_save now use readRDS and saveRDS instead of load and save. This is the right approach to serialize single R objects. If you need a script to convert previously saved datasets (created using nmr_dataset_save) please use NIHSnmr:::nmr_dataset_load_old_and_save(“your_old_file.RData”, “your_old_file.RDS”) to convert the files. Sorry for the inconvenience, but the sooner we fix this the better.

• filter to select a subset of samples from an nmr_dataset object has been adapted to dplyr >= 0.7.4. Unless you used the .dots argument in your calls there is no need to change anything. This means we now use a tidy evaluation syntax for filter.

• nmr_get_metadata() returns always a data frame / tibble, even when only a single column is requested. It also always includes the “NMRExperiment” column.

• nmr_dataset object has two tables metadata and metadata_ext. The metadata_ext table includes all the metadata we add with nmr_add_metadata while metadata has the internal metadata (acquisition parameters, etc). Please use nmr_get_metadata(nmr_dataset) instead of nmr_dataset$metadata.

Other changes

• Remove workaround to dplyr issue: https://github.com/tidyverse/dplyr/issues/2203 (Sergio Oller reported and fixed the issue, dplyr-0.7.0 is fixed)

• The Bruker title file has quite a free format definition. A title file can contain lines like “Field value” or “Field value ;” or simply “value”. The heuristics to parse the title file have been improved.

• Depend on tidyr 0.8.1. tidyr 0.8.0 had a bug that we reported (and for which we also provided a fix): https://github.com/tidyverse/tidyr/pull/419

• nmr_get_metadata gives a warning if the user asks for metadata columns that are missing.

• New nmr_integrate_regions function.

• nmr_normalize accepts pqn normalization.

ANCOMBC

             Changes in version 0.99.5 (2020-10-19)                 

• Update README

             Changes in version 0.99.4 (2020-09-26)                 
  

• Update README

             Changes in version 0.99.3 (2020-09-13)                 
  

• Using the GlobalPatterns dataset in the examples

             Changes in version 0.99.2 (2020-09-05)                 
  

• Integrating with phyloseq-class experiment-level object

             Changes in version 0.99.1 (2020-08-23)                 
  

• Addressed reviewer’s comments

             Changes in version 0.99.0 (2020-08-10)                 
  

• Submitted to Bioconductor

AnnotationHub

                   Changes in version 2.21.0                        

BUG FIX

• (2.21.5) Fix documentation for setting AnnotationHubOptions

• (2.21.3) Fix printing of proxy when present

USER-VISIBLE MODIFICATIONS

• (2.21.6) Make internet connection test less stringent

• (2.21.4) Add link to github for reporting issues

• (2.21.2) Update to reference hubs@bioconductor.org for help

• (2.21.1) Update .tidyGRanges to account for incorrect or missing genomes

AnnotationHubData

                   Changes in version 1.19.0                        

INTERNAL BUG CORRECTION

• 1.19.2 Update Metadata from Ensembl function to use GenomeInfoDb:::fetch_species_index_from_Ensembl_FTP instead of parsing the file path

• 1.19.1 misplaced ! clause

annotatr

                   Changes in version 1.16.0                        

USER-FACING CHANGES

• Export expand_annotations(), tidy_annotations(), and subset_order_tbl().

BUGFIXES

• Fix incorrect shortcut search for HMMs.

AnVIL

                    Changes in version 1.2.0                        

NEW FEATURES

• (v 1.1.3) introduce .deprecated flag in operations() / tags(); don’t include deprecated APIs by default; warn on use of deprecated APIs.

• (v 1.1.4) add repositories() to return binary (if available), Bioconductor, and CRAN repository paths.

• (v 1.1.6) provide md5sum as check on service version.

• (v 1.1.9) add avfiles_*() for managing workspace bucket files.

• (v 1.1.15) add avtable_import_set() to create subsets of tables, following the Terra data model.

• (v 1.1.16) add avruntimes(), avworkspace_jobs() to query for runtimes and jobs associated with the active billing account.

• (v 1.1.17) add avdisks() to query for persistent disks associate with the active billing account.

• (v 1.1.21) add avworkflow_*() for interacting with workflow jobs and outputs.

AnVILBilling

                   Changes in version 0.0.12                        

• pass CMD check and BiocCheck

                   Changes in version 0.0.11                        
  

• removes browse_reck parameters, encapsulates authentication better

                   Changes in version 0.0.10                        
  

• New parameter to browse_reck() that defaults to NOT running bq_auth explicitly. Now only one authentication per session is performed if do_auth is FALSE

                    Changes in version 0.0.9                        
  

• Plots in plot tab are now plotly for pointwise segmented display, and simple cumulative display

                    Changes in version 0.0.7                        
  

• No warnings on R CMD check or BiocCheck; one ERROR concerning support site registration
• Includes browse_reck(), an app that tabulates expenses over time
• Updates to vignette, including demonstrative static graphics
• It seems that the page_size parameter does not properly propagate to BigQueryConnection; documenting this will take time; for now avoid querying for long intervals of time

AnVILPublish

                   Changes in version 0.0.10                        

• Add ‘best practices’ and rationale for Rmarkdown-to-jupyter notebook conversion.

                    Changes in version 0.0.9                        
  

• Create a notebook ‘00-«workspace name»’ to install package / book dependencies specified in the original source.
• Don’t link to vignettes from the DASHBOARD, since the namespace changes in cloned workspaces.

• as_workspace(…, create = FALSE, update=FALSE) now evaluates code, silently.

                    Changes in version 0.0.8                        
  

• Support collections of Rmd files that are not packages, e.g., bookdown sites.

• Add R / Bioconductor version to dashboard

                    Changes in version 0.0.7                        
  

• Revise Rmd-to-ipynb work flow

• Don’t evaluate code chunks (avoids including output in notebook, and side-effects because rmarkdown::render does not start a separate process)

• Insert metadata to use the R kernel. jupytext can do this more elegantly, but does from .md renders code chunks and pre-formatted rather than evaluation cells, and from .Rmd does not process markdown well enough, e.g., not suppporting [foo][]-style links when the definition is elsewhere in the document.

                    Changes in version 0.0.6                        
  

• Added a NEWS.md file to track changes to the package.

• Extensive interface renaming

• as_workspace() (formerly package_source_as_workspace())
• as_notebook() (formerly vignettes_to_notebooks())
• add_access() (formerly bioconductor_user_access())

APAlyzer

             Changes in version 1.3.3 (2020-07-20)                  

• Fixed hg38_REF.RData.

             Changes in version 1.3.2 (2020-07-20)                  
  

• Updated the CITATION.

             Changes in version 1.3.1 (2020-07-19)                  
  

• Fixed the interval issues in hg38_REF.RData and mm10_REF.RData.

• Updated the CITATION.

artMS

             Changes in version 1.6.7 (2020-10-22)                  

• The following plots are now deprecated

• .clustering.log2fcSign.all-zoom.pdf

• .clustering.log2fc.all-zoom.pdf

• Fix bugs

             Changes in version 1.6.6 (2020-10-21)                  
  

• Convert new MaxQuant format of PTMs to the old format

• MSstats messages are not displayed by default when using artmsQuantification. The user can enable MSstats messages by selecting “display_msstats = TRUE”

• Prevent artmsWriteConfigYamlFile() from overwriting an existing configuration file unless the user allows it (overwrite = TRUE)

• printPDF now available in all functions printing plots to pdf, which means that notebooks can be used and print all plots. Default is still printPDF = TRUE

• Fix bugs

             Changes in version 1.6.5 (2020-05-20)                  
  

• Fix ggplot warnings (caused by NA values)

• Fix artmsAnalysisQuantification reproducibility plots

• Improves artmsQualityControlEvidenceBasic() correlation matrix clustered plot

• Fix pca01.pdf plot

• New pca04.pdf plot (dot plot)

• artmsAnalysisQuantifications check point: check if sufficient data is available

             Changes in version 1.6.4 (2020-05-12)                  
  

• Fix Quality Control functions to handle a small number of runs (less than 5)

• New argument “printPDF” for artmsQualityControlSummaryExtended, to select whether to print plots to PDFs (default = TRUE)

• Vignette: example plots added

             Changes in version 1.6.3 (2020-05-06)                  
  

• Bug Fixes affecting artmsAnalysisQuantifications()

             Changes in version 1.6.2 (2020-05-05)                  
  

• Fix NEWS formatting

• Update vignette with AC options

             Changes in version 1.6.1 (2020-04-29)                  
  

• Fix NEWS formatting

• Update vignette with AC options

ASpli

                   Changes in version 1.99.3                        

NEW FUNCTIONS AND FUNCTIONALITIES

• New parameters for gbCounts and jCounts functions:

• libType: to specify single end (“SE”) or paired end (“PE”) library

• strandMode:

  • 0: strand of the pair is always *.
  • 1: strand of the pair is strand of its first alignment

  • 2: strand of the pair is strand of its last alignment.

                   Changes in version 1.99.1                        
    

NEW FUNCTIONS AND FUNCTIONALITIES

• For counting: gbCounts and jCounts. We add library type and strand-specificity parameters.

• For DU estimation: DUreport.norm and DUreport.offset

• For prepare DU reports: filterSignals, gbDUreport, integrateSignals, jDUreport, splicingReport and junctionsPJU

• For printing reports: exportIntegratedSignals, writeJDU and writeSplicingReport

FUNCTIONS DEPRECATED

• loadBAM: will be replaced by gbCounts. Bams files are proccesed one by one, according target object. It improves running time and memory usage

• readCounts: it is replaced by gbCounts

• AsDiscover: it is replaced by jCounts

• DUreport: it is replaced by gbDUreport and jDUreport

• mergeBinDUAS: has no direct replacement.

• plotGenomicRegions: has not direct replacement. There are new functions for exportiing results into HTML pages.

AssessORF

             Changes in version 1.7.1 (2020-10-23)                  

• Genome viewer plots will now show the forward strand above the reverse strand, and reading frames will now be laid out in 1 through 6 order moving down the genome viewer (before it was reversed)

             Changes in version 1.7.0 (2020-10-21)                  
  

• Can now toggle interactivity of the genome viewer when plotting Assessment objects

• Can now zoom into an initial range with the genome viewer when plotting Assessment objects

• Documented the genome viewer in the plot.Assessment man page

• Added a genome viewer example to the vignette

• Fixed a bug that was causing an error when users attempted to zoom out ten-fold with the genome viewer plot

ATACseqQC

                   Changes in version 1.13.9                        

• fix the issue that plotCorrelation heatmap is scaled by row.

                   Changes in version 1.13.8                        
  

• throw an error if not enought nucleosome free read nor mononucleosome reads for training.

                   Changes in version 1.13.7                        
  

• fix a bug introduced by matchPWM by paste ^ and $ into exclude sequence name.

                   Changes in version 1.13.6                        
  

• update documentation of plotFootprints.

                   Changes in version 1.13.4                        
  

• fix a formular for TSSE score.

                   Changes in version 1.13.3                        
  

• fix a bug the after shift, the index is not changed.

                   Changes in version 1.13.2                        
  

• change the normalization method by library size for factorFootprints for user defined group samples.

                   Changes in version 1.13.1                        
  

• Add documentation to decribe the format of bindingSites for factorFootprints.

Autotuner

             Changes in version 1.3.0 (2020-09-24)                  

• Updated the required version of dependencies

• Added flag for plot peaks courtesy of John Bouranis

BANDITS

                    Changes in version 1.4.1                        

• parallel::makeCluster() updated to “sequential” strategy; default strategy gets stuck with RStudio on macOS with R 4.x.

BASiCS

             Changes in version 2.1.16 (2020-10-22)                 

• Updates .BASiCS_MCMC_Start to use different starting values when an empirical Bayes prior is assigned to mu

• Adds log_scale parameter to .EmpiricalBayesMu

• Fixes small bug in .BASiCS_MCMC_Start

• Updates unit tests linked to the change in .BASiCS_MCMC_Start

• Adds fixed seeds to test_divide_and_conquer.R

             Changes in version 2.1.14 (2020-10-08)                 
  

• Add support for divide and conquer inference with BASiCS_DivideAndConquer function. Add support for this function to BASiCS_MCMC

• Add BASiCS_MockSCE function to create a SingleCellExperiment object with arbitrary dimensions.

• Fix Makevars warning relating to PKG_CXXFLAGS

             Changes in version 2.1.13 (2020-10-05)                 
  

• Add PriorParam argument to BASiCS_MCMC

             Changes in version 2.1.12 (2020-10-01)                 
  

• Remove unused DelayedArray call from tests

             Changes in version 2.1.11 (2020-09-30)                 
  

• Updated documentation for Threads in BASiCS_MCMC to indicate default value.

             Changes in version 2.1.10 (2020-09-30)                 
  

• Documents Threads argument.

             Changes in version 2.1.9 (2020-09-28)                  
  

• Add Threads argument to BASiCS_MCMC, allowing parallelisation of MCMC updates across cells or genes using openMP.

• Reduce BatchInfo requirement for no spikes sampler to a warning, from an error.

             Changes in version 2.1.8 (2020-09-28)                  
  

• Minor edit in the vignette to recommend the use of a seed for reproducible results when using BASiCS_MCMC.

             Changes in version 2.1.7 (2020-09-23)                  
  

• Bugfix in format method for ResultVG class.

• For BASiCS_PlotDE, if only one plot is produced, the plot is returned as a bare ggplot object rather than using cowplot::plot_grid

• Added EpsilonThreshold argument for BASiCS_DetectHVG and BASiCS_DetectLVG. This uses a threshold on epsilon values to identify LVGs and HVGs. Also adds a MinESS argument to BASiCS_DetectHVG and BASiCS_DetectLVG.

• Deprecated newBASiCS_Data and the format methods for Results classes. For the latter, use as.data.frame instead.

• Improved documentation for BASiCS_ResultVG class

• BASiCS_MCMC now computes and stores ESS as an attribute of parameter matrices when sampling has completed.

• Make use of Parameter argument consistent across several methods, where Param and Which were used before.

• Extended BASiCS_DiagPlot to enable other diagnostic measures

• Moved to store molecule counts in rowData(altExp(sce)) rather than metadata(sce)

• Remove dependency to KernSmooth

• Set some values to NA if they relate to genes captured in < 2 cells

• Add option to exclude spike-ins in BASiCS_DenoisedCounts. Also use a slightly more principled calculation internally.

• See issues #182, #39, #91, #169, #181, #178, #202, #190, #173

             Changes in version 2.1.6 (2020-08-05)                  
  

• Prevents usage of BASiCS_VarThresholdSearchVG when using residual overdispersion parameters

             Changes in version 2.1.5 (2020-08-05)                  
  

• Minor change on the definition of OrderVariable within BASiCS_DetectVG

             Changes in version 2.1.4 (2020-08-05)                  
  

• Extended unit tests to verify the validity of input parameters for BASiCS_DetectLVG and BASiCS_DetectHVG.

• Updated documentation for BASiCS_DetectVG to account for new default values and the type of output (now object with class BASiCS_ResultVG).

• Unit tests for LVG updated as new default value for ProbThreshold is used whenever the EFDR calibration fails (2/3 as opposed to 0.5).

• Minor changes in BASiCS_VarThresholdSearch to avoid errors in the presence or absence of epsilon. This function is likely to be deprecated.

• Updates default probability threshold in .ThresholdSearch when EFDR calibration fails. This is now set to ProbThreshold (not 0.9)

             Changes in version 2.1.3 (2020-07-29)                  
  

• New default values for PercentileThreshold (= NULL), VarThreshold (= NULL) and ProbThreshold (= 2/3) in BASiCS_DetectVG). The latter is compatible with the default values in BASiCS_TestDE.

• Changes default behaviour of BASiCS_DetectLVG, BASiCS_DetectHVG in accordance with the changes introduced for BASiCS_DetectVG.

             Changes in version 2.1.2 (2020-07-29)                  
  

• Moves auxiliary functions related to HVG/LVG analysis to utils_VG.R. This includes .VGPlot, .VGGridPlot, .HeaderDetectHVG_LVG and .VG.

• Updated warning messages in .HeaderDetectHVG_LVG

• Updated rules for EFDR and ProbThreshold parameters in BASiCS_DetectVG. If EFDR = NULL, EFDR calibration is not used and posterior probability threshold is set to be equal to ProbThreshold. This behaviour is consistent with the rules used in BASiCS_TestDE.

• Creates .CheckProbEFDR to perform validity checks for ProbThreshold and EFDR in all tests (HVG/LVG and DE).

• Cleans code within .ThresholdSearch and BASiCS_DetectVG

• Removes Threshold from the output provided by BASiCS_DetectVG

• Removes duplicated plotting code in BASiCS_DetectVG. Now calls BASiCS_PlotVG.

• Changes .VGGridPlot and .VGPlot to use ggplot2:theme_classic()

             Changes in version 2.1.1 (2020-07-28)                  
  

• Bugfix in BASiCS_DetectHVG and BASiCS_DetectLVG. Epsilon/Delta,Sigma values were erroneously not returned.

• More detailed colouring of differential expression plots.

• Bugfix in labels for DE plots.

basilisk

                    Changes in version 1.2.0                        

• Added support for different Conda channels in the BasiliskEnvironment() constructor.

• Added locking to setupBasiliskEnv() for safe parallel construction of environments.

• Ensure that environments are always activated before use in useBasiliskEnv().

basilisk.utils

                    Changes in version 1.2.0                        

• Migrated most environment-related functions to basilisk.

• Added locking to installConda() for safe parallel lazy Conda installations.

• Switched to the latest Miniconda3 installer.

batchelor

                    Changes in version 1.6.0                        

• Allow regressBatches() to operate without batch= when design= is provided. Added d= and related options to conveniently perform a PCA on the ResidualMatrix.

• Added correct.all= option to all correction functions for consistency.

• Added a deferred=TRUE default to multiBatchPCA and its callers, to encourage use of deferred matrix multiplication for speed.

• Switched default PCA algorithm in multiBatchPCA to IrlbaParam.

• Added add.single= mode for endomorphic addition of correction results in correctExperiments().

BayesSpace

                   Changes in version 0.99.8                        

Minor improvements and fixes

• spatialCluster() and spatialEnhance() now use a faster implementation of the multivariate normal density that reduces runtime by approximately 40%.

                   Changes in version 0.99.7                        
  

Minor improvements and fixes

• Documentation examples now use fewer iterations in order to reduce the runtime of R CMD check.

• In qTune(), the min_rep and max_rep parameters have been replaced with burn.in and nrep, respectively, to be consistent with spatialCluster().

                   Changes in version 0.99.6                        
  

New features

• getRDS() gains a cache parameter. When TRUE, the RDS is cached locally using BiocFileCache.

Minor improvements and fixes

• Addressed reviewer concerns (https://github.com/Bioconductor/Contributions/issues/1624)
• Updated stop/warning/message statements to remove redundancies and unnecessary use of paste().
• Removed inline conditional statements.
• Cache downloaded RDS in getRDS() (see above).
• spatialCluster() and spatialEnhance() handle the edge case where only one iteration is kept after excluding burn-in.
• The coda::mcmc object returned by mcmcChain() now specifies the thinning interval used in enhanced objects.
• spatialCluster() and spatialEnhance() now include platform-specific defaults for the gamma parameter.

• Minor internal refactoring.

                   Changes in version 0.99.5                        
  

Minor improvements and fixes

• In spatialCluster() and spatialEnhance(), setting burn.in equal to nrep now raises an error.

                   Changes in version 0.99.4                        
  

New features

• enhanceFeatures() now takes an nrounds parameter that corresponds to the same parameter in xgboost. If nrounds is set to 0, we automatically tune the parameter using a train/test split for improved feature prediction.
• spatialCluster() and spatialEnhance() both gain a burn.in parameter specifying the number of MCMC iterations to exclude when aggregating cluster labels and enhanced PCs.
• In clusterPlot(), label now accepts factors and vectors of strings, in addition to numeric vectors or a column name in colData.
• Additional vignettes provided for reproducing the analyses of the melanoma, dorsolateral prefrontal cortex, and squamous cell carcinoma datasets presented in the bioRxiv manuscript.

Minor improvements and fixes

• The internal layout of subspots is now correctly oriented (accounting for vertical flip of spot coordinates) when using spatial plot functions on enhanced Visium data.
• In spatialEnhance(), PCs are now averaged over the MCMC iterations (excluding the burn-in period).
• In enhanceFeatures(), negative expression is now clipped to 0.
• spatialPreprocess() now adds a boolean is.HVG column to rowData.

• In featurePlot(), additional arguments to geom_polygon() are correctly passed through.

                   Changes in version 0.99.3                        
  

Minor improvements and fixes

• Updated README.md to include system requirements, additional installation details, and link to vignette with demonstration of package functions, per journal guidelines.

                   Changes in version 0.99.2                        
  

Minor improvements and fixes

• spatialEnhance() incorrectly added row offset to spot column coordinate when generating subspot colData, and vice versa. This resulted in subspots being reflected over y=x in spatial plots, and has been fixed.

• Figures in the demonstration vignette have been updated with this fix.

                   Changes in version 0.99.1                        
  

Minor improvements and fixes

• Removed Maintainer field from DESCRIPTION to adhere to Bioconductor guidelines.

                   Changes in version 0.99.0                        
  

New features

• Initial Bioconductor submission

BgeeCall

                    Changes in version 1.5.3                        

• Add function generate_slurm_indexes generating kallisto indexes on a cluster with slurm queing system

• Add function generate_slurm_calls generating expression calls on a cluster with slurm queing system

• Update documentation

• Add ?BgeeCall documentation with link to main functions

BgeeDB

                   Changes in version 2.14.1                        

• Solve download timeout with Windows

bigPint

             Changes in version 1.5.1 (2020-08-23)                  

plotClusters() function now has option for superimposing pairs or whole data using the showPairs parameter.

BiocCheck

                    Changes in version 1.25                         

DEPRECATION ANNOUNCEMENT

• (1.25.11) R CMD BiocCheck and R CMD BiocCheckGitClone are deprecated. The recommended way to run the functions is within R.

NEW FEATURES

• (1.25.4) Check for single colon typos when using qualified imports pkg::foo()

• (1.25.1) Check for warning/notes on too-brief a Description: field (@federicomarini, #65)

• (1.25.8) Validate ORCID IDs (if any) in the DESCRIPTION file (@LiNk-NY, #97)

• (1.25.10) Add check for properly formatted CITATION file

• (1.25.12) Add NOTE to change dontrun to donttest

BUG FIXES

• (1.25.14) The ORCID ID check now accepts IDs with a X at the end.

• (1.25.9) All packages including infrastructure require a vignette

• Usage of donttest and dontrun in manual pages tagged with the keyword ‘internal’ will no longer trigger a NOTE (@grimbough, #59)

• (1.25.7) Adding the sessionInfo at the end of the vignette (@llrs)

USER SIGNIFICANT CHANGES

• (1.25.3) Require Aurhors@R format over Author/Maintainer fields in the DESCRIPTION file. This has been upgraded to an ERROR.

• (1.25.2) Resolve https://github.com/Bioconductor/BiocCheck/issues/57: Suggest styler over formatR for automatic code re-formatting.

• (1.25.5) Add warning to new package versions with non-zero x version (@mtmorgan, #101)

BiocParallel

                    Changes in version 1.24                         

BUG FIXES

• (v.1.23.1) bpvalidate() detects variables defined in parent environments; warns on use of global variables.

• (v.1.23.2) bplapply() runs gc() after each evaluation of FUN(), so that workers do not accumulate excessive memory allocations (memory on a per-process basis is not excessive, but cluster-wise could be). See https://github.com/Bioconductor/BiocParallel/pull/124:x

BiocSet

                     Changes in version 1.3                         

BUG FIX

• (1.3.5) Improve GeneSetCollection functionality.

• (1.3.3) Fix failing tests for kegg_set().

• (1.3.1) Fix failing tests due to new version of GO.db.

NEW FEATURES

• (1.3.6) Made the switch from import/export functionality in rtracklayer to BiocIO.

• (1.3.4) Extending our export functionality to allow for OBO files. Also create functions to disply relationships of an OBOSet object.

• (1.3.2) Extending our import functionality to allow for OBO files.

BiocSingular

                    Changes in version 1.6.0                        

• Migrated the ResidualMatrix class to its own ResidualMatrix package.

biocthis

                   Changes in version 0.99.0                        

NEW FEATURES

• Added a NEWS.md file to track changes to the package.
• Added bioc_style() which provides a partial Bioconductor coding style compatible with styler.
• Added usethis-style functions use_bioc_citation(), use_bioc_description(), use_bioc_github_action(), use_bioc_issue_template(), use_bioc_news_md(), use_bioc_pkg_templates(), use_bioc_readme_rmd(), use_bioc_support() and use_bioc_vignette(). These functions provide Bioconductor-friendly alternatives to several functions in the usethis package.
• use_bioc_github_action() allows you to use a Bioconductor-friendly GitHub Actions workflow for checking your Bioconductor package (or one that depends on Bioconductor packages). Check the vignettes for details on its features as well as the developer notes.

biocViews

                   Changes in version 1.57.0                        

NEW FEATURES

• (1.57.5) New views AnnotationHubSoftware and ExperimentHubSoftware

BUG FIX

• (1.57.4) In NEWS generation, fix formatting.

• (1.57.1) In VIEWS generation fix but with vignetteTitles. When combinding different format types could potentially remove vignette titles that ended with “RNA,”. Do strict start of and end of string check for formatting.

biomaRt

                   Changes in version 2.46.0                        

BUG FIXES

• getLDS() now detects if trying to use datasets from different Marts and reports this to the user.

BioMM

                    Changes in version 1.5.7                        

• Improved description in the tutorial (BioMM() function returns the prediction scores instead of metrics)

• Updated BioMMstage2pred() and BioMM() functions to get prediction scores instead of performance metrics

• Updated getMetrics() to cope with the ‘probability’ predicted score as well.

                    Changes in version 1.5.4                        
  

• Improved description in the tutorial

                    Changes in version 1.5.2                        
  

• updated R functions for reporting results and plotting.

• added another omics data (gene expression) and KEGG pathway.

• updated tutorial by demonstrating BioMM with another omics data (gene expression) and KEGG pathway annotation.

biosigner

                   Changes in version 1.17.2                        

MINOR MODIFICATION

• getMset: minor correction in documentation

BrainSABER

             Changes in version 0.99.0 (2020-02-14)                 

• *submitted to Bioconductor

breakpointR

                    Changes in version 1.7.2                        

• Added new function to allow for removal of spikes in read coverage present in composite files.

                    Changes in version 1.7.1                        
  

• Added new deltaW calculator that allows to define multiplication of the original window size to use for deltaW calculations. One can invoke this by setting ‘multi.sizes’ parameter.

BRGenomics

                    Changes in version 1.1.3                        

• Increased safeguards against automatic vector coercion of matrices and dataframes
• Increased tolerance of the precision workaround in getStrandedCoverage() (workaround releveant to GenomicRanges issue #39; will be obviated in next major Bioconductor release)

• Various minor efficiency & formatting changes

                    Changes in version 1.1.1                        
  

• Merge changes from 0.99.33 into release branch
• Bug workaround for getStrandedCoverage() and dependent methods for getting coverage of normalized data (apparent bug in IRanges::coverage() for weighting by normalized values)
• Bug fix in getCountsByPositions() for getting counts over an unstranded region with expand_ranges=TRUE

BridgeDbR

                   Changes in version 1.99.1                        

BUG FIXES

• no more downloading of databases in the examples

                   Changes in version 1.99.0                        
  

BUG FIXES

• Added missing NEWS section for 1.23.1

• BridgeDb 3.0.0-SNAPSHOT (2020-10-18)

                   Changes in version 1.23.1                        
  

SIGNIFICANT USER-LEVEL CHANGES

• no longer supports 32bit on Windows

CAGEr

                   Changes in version 1.31.4                        

BUG FIXES

• Update end coordinates before start coordinates in the function .aggregateTagClustersGR(). This should stop triggering “‘width(x)’ cannot contain negative integers” errors.

                   Changes in version 1.31.3                        
  

BUG FIXES

• Correct .make.consensus.clusters internal function. This should stop triggering “Consensus clusters must not overlap with each other” errors.

                   Changes in version 1.31.2                        
  

BUG FIXES

• Allow empty CTSS.chr objects.

• Correct plotInterquantileWidth() to really use consensus clusters when passed the argument `clusters = “consensusClusters”.

• Fix failures on CAGEexp objects containing only one sample.

CAMERA

                   Changes in version 1.45.2                        

BUG FIXES

• Thanks to Sebastien Hutinet @shutinet for fixing the adduct mass of CF3COOH. Includes a corresponding change in unit tests. Closes #61

Cardinal

             Changes in version 2.7.2 (2020-10-21)                  

SIGNIFICANT USER-VISIBLE CHANGES

• For ‘mzAlign()’, the ‘ref’ parameter now expects a vector of reference m/z-values rather than a complete spectrum

                    Changes in version 2.7.1                        
  

BUG FIXES

• Fixed issue where ‘spatialDGMM()’ would sometimes fail for features with singular segmentations

• Suppressed warnings on ‘Mclust()’ initialization to ‘spatialDGMM()’ caused by R 4.0 changes

• Fixed pixel/feature mapping in ‘spatialDGMM()’ metadata

cbaf

             Changes in version 1.12.0 (2020-04-08)                 

New Features

• Terms are updated. Package can recongize even more cancer studies!

• Improvements for methylation analysis.

• If desired genes are entered as a vector, they are converted to a list without returning an error.

cBioPortalData

                    Changes in version 2.2.0                        

New features

• studiesTable includes additional columns pack_build and api_build to indicate to the user which datasets have been successfully build as MultiAssayExperiment objects. Users will be notified when a dataset reported as not building is input to the cBioDataPack function.
• Add sampleIds argument to getDataByGenePanel as part of cache re-work
• Allow more flexibility in the hostname when accessing the API with cBioPortal (@inodb, #16)
• cBioDataPack downloads from a more robust repository (AWS S3; @inodb, #22)
• removePackCache and removeDataCache now remove data from the user’s cache based on inputs to respective functions (cBioDataPack and cBioPortalData)

Bug fixes and minor improvements

• Attempt to merge additional clinical data files from tarballs in cBioDataPack.
• Switch to using read.delim instead of read_tsv internally to avoid assigning NA to chromosome column
• Use ‘PATIENT_ID’ when available to determine if experiment data is provided in the tarball files.
• Add tests using testthat
• Update and include percentages of studies successfully imported using cBioDataPack and cBioPortalData in the documentation
• Fix read-in when identifiers are numeric instead of character (@jucor, #27)
• Include pagination parameters in geneTable function (@xinwei-sher, #29)

CellaRepertorium

             Changes in version 0.99.0 (2020-09-28)                 

Submitted to bioconductor.

CellTrails

                    Changes in version 1.7.1                        

• Compatible with R 4.0.0

• Bugfixes:

  • Removed isSpike
  • Resolved error with extracting latent space information at ‘showTrajInfo’
  • Resolved inverted color palette for ‘plotManifold’ and ‘plotMaps’
  • Resolved machine precision issue for ‘findStates’

CeTF

                    Changes in version 1.0.2                        

• Fix netConditionsPlot function bugs

cfDNAPro

                   Changes in version 0.99.1                        

• Remove bugs in plotSingleGroup.R

• Documentation improvements.

                   Changes in version 0.99.0                        
  

• Now cfDNAPro supports bam file as input for data characterisation.
• Coding style improvements.
• Documentation improvements.
• Submitted to Bioconductor.

ChAMP

                   Changes in version 2.18.2                        

• Added parallel running for ebGSEA function. And allow it to return enriched gene list.

Chicago

             Changes in version 1.17.1 (2020-09-08)                 

• Fixed a small bug that affected distance function estimation in some cases, particularly when used with four-cutter enzymes.

ChIPpeakAnno

                   Changes in version 3.23.12                       

• fix the bug for genomicElementDistribution when the order of SortedByQueryHits is incorrect.

                   Changes in version 3.23.11                       
  

• use seqlevelsStyle to reformat the seqlevels for annotation.

                   Changes in version 3.23.10                       
  

• update documentation for genomicElementDistribution

                   Changes in version 3.23.9                        
  

• add new function enrichmentPlot, genomicElementDistribution, genomicElementUpSetR, and methagenePlot to improve visualization.

                   Changes in version 3.23.8                        
  

• update documentation for findOverlapsOfPeaks.

                   Changes in version 3.23.7                        
  

• update documentation for findOverlapsOfPeaks.

                   Changes in version 3.23.6                        
  

• change parameter from otherCount to otherCounts to makeVennDiagram function.

                   Changes in version 3.23.5                        
  

• add plot parameter to makeVennDiagram function.

                   Changes in version 3.23.4                        
  

• update README file.

                   Changes in version 3.23.3                        
  

• use roxygen2 to generate the help file.

• move multiple package from Imports to Suggests.

                   Changes in version 3.23.2                        
  

• fix the issue for new paste output.

                   Changes in version 3.23.1                        
  

• remove dependence of Rfast

ChIPQC

                   Changes in version 1.25.1                        

• Update to maintain compatibility with DiffBind 3.0

ChromSCape

             Changes in version 0.99.0 (2020-10-23)                 

• Submitted to Bioconductor

chromstaR

                   Changes in version 1.14.2                        

BUG FIXES

• Corrected format check for experiment.table: Spaces are not excepted any longer, because they lead to downstream errors.

                   Changes in version 1.14.1                        
  

BUG FIXES

• Compatibility update: Replaced class() checks with is().

CHRONOS

                   Changes in version 1.17.2                        

• Introduced the use of rJava in getLinearSubpath().

• Introduced futures in class LinearPaths.

circRNAprofiler

                    Changes in version 1.3.1                        

Added files to fix bugs

cleanUpdTSeq

                   Changes in version 1.27.1                        

• update the classifier dataset

cleaver

             Changes in version 1.27.1 (2020-06-05)                 

• Fix cleavage rule for glutamyl endopeptidase in documentation Thanks to Mariia Chernigovskaya mariia.chernigovskaya@medisin.uio.no for reporting this error.

clusterProfiler

                   Changes in version 3.17.5                        

• update [[.compareClusterResult (2020-10-14, Wed)

                   Changes in version 3.17.3                        
  

• internal suports of enrichment analyses using WikiPathways (2020-09-09, Wed)
• enrichWP for ORA analysis
• gseWP for GSEA analysis
• get_wp_organisms for listing supported organisms

• read.gmt.wp for parsing gmt file downloaded from wikiPathways

                   Changes in version 3.17.2                        
  

• use libcurl if capable (2020-09-08, Tue)

• https://github.com/YuLab-SMU/clusterProfiler/pull/290

                   Changes in version 3.17.1                        
  

• bug fixed of extract_params (2020-08-18, Tue)
• https://github.com/YuLab-SMU/clusterProfiler/issues/282

clustifyr

             Changes in version 1.1.2 (2020-09-21)                  

• USCS cell browser reference building

• Tutorial update

• Bug fixes

             Changes in version 1.1.0 (2020-05-21)                  
  

• Bioc release

• Bug fixes

CNVPanelizer

                   Changes in version 1.21.2                        

• Moving BiocGenerics at DESCRIPTION from Suggests to Imports

cola

                    Changes in version 1.5.5                        

• add enforce argument in get_signatures().

• subset can be a vector of indices in consensus_partition_by_down_sampling().

                    Changes in version 1.5.3                        
  

• predict_classes() is speeded up 2x.

• get_signatures(): add top_signatures argument to control the number of top signatures.

                    Changes in version 1.5.2                        
  

• add a DownSamplingConsensusPartition class and corresponding methods.

• add back HierarchicalPartition class and corresponding methods.

                    Changes in version 1.5.1                        
  

• add a predict_classes() function.

• add the cola analysis for Golub dataset as a data object in the package.

• automatically install the “suggested” packages.

ComplexHeatmap

                    Changes in version 2.5.6                        

• ht_shiny(): add argument app.

• grid.dendrogram(): change the recursive implementation with iterations.

• change default raster device to CairoPNG.

• Heatmap(): If the discrete col covers more than the levels in the matrix, the full color set is still saved, which means, in heatmap_legend_param you can set at that are not all in the matrix but are in the col.

• padding of the whole plot and spaces of column titles are adjusted to fit ggplot2

• add row_gap and column_gap in Legend().

• oncoPrint(): now draw legends the same as alter_fun.

• add a new function attach_annotation().

• legends for row annotations can be grouped with column annotation legends.

• annotation name allows rotations.

                    Changes in version 2.5.5                        
  

• still draw the legend when all values are NA in an annotation.

• add show_fraction argument in anno_oncoprint_barplot() function to show the fractions of mutations instead of the counts.

• pheatmap(): improve the setting of color and breaks.

• ht_opt$TITLE_PADDING can be set with a unit of length two.

• HeatmapAnnotation(): remove colors that are not in the annotations.

• pheatmap(): fixed a bug when length(breaks) = length(color) + 1

• pheatmap(): legend breaks are centered to zero if the matrix is scaled.

• pheatmap(): color mapping is symmetric to zero when scale is set.

• support ragg package to write temporary png files

• densityHeatmap(): column dendrogram is reordered by column means for ks method.

                    Changes in version 2.5.4                        
  

• fixed a bug where slice clusters were wrongly reordered.

• Heatmap(): add border_gp argument.

• Legends are nicely placed.

• anno_block(): allows to set height and width.

• support better rasterization.

• support setting graphics on dendrogram nodes.

• Add a new vignette “interactive heatmap”

• Legends(): fixed a bug of mixtype “legend” to “Legend”.

• now assign correct envir to decorate_dend().

• pheatmap(): check NA in the matrix.

• grid.dendrogram(): consider branches with height zero.

• checking the dimension of the matrix and the nobs of annotations when adding them.

                    Changes in version 2.5.3                        
  

• add selectArea()/selectPosition() which allows interactively select a region from the heatmaps.

• export the heatmap as a shiny app!!!

• col in Heatmap() accpets a ColorMapping object.

• default_col(): print a message if there are outliers in the matrix.

• discrete_legend_body(): adjust ncol and nrow if there are empty rows and columns in the layout.

• anno_image(): fixed a bug that images are not reordered.

• anno_mark(): now expression is correctly supported.

• anno_zoom(): order of index in panel_fun is adjusted to the order in the heatmap

• list_to_matrix(): convert elements to characters.

• print messages for anno_mark(), anno_zoom(), draw_legend() (if legends are wrapped) if working under RStudio.

                    Changes in version 2.5.2                        
  

• translate pheatmap to Heatmap

• upset_top_annotation() and upset_right_annotation(): the names of the annotations are changed to intersection_size, set_size and union_size.

• list_components(): adds pattern argument.

                    Changes in version 2.5.1                        
  

• A temporary solution of the sum of two complicated units (in temp.R).

CoreGx

                    Changes in version 1.1.5                        

• Implemented a new class, the LongTable, to store the results of a treatment response experiment. This class provides a flexible and fast data storage object which can be subclassed for use in other R packages.

• Added vignette documenting LongTable accessors and usage of the new object.

                    Changes in version 1.0.2                        
  

• Bug fix: suppress warnings thrown by piano::runGSA inside the connectivitScore function

                    Changes in version 1.0.1                        
  

• Updated the CoreGx vignette to include more information on extending the CoreSet class for use in other treatment-response experiments.

CRISPRseek

                   Changes in version 1.29.2                        

• added parameters such as predIndelFreq to allow the prediction of indels and their frequecies for Cas9 targeted sites

                   Changes in version 1.29.1                        
  

• added parameter calculategRNAefficacyForOfftargets, default to TRUE.

csaw

                   Changes in version 1.24.0                        

• Accept a list of BamFiles in bam.files= for all functions.

cTRAP

                     Changes in version 1.8                         

Interactive functions for loading data and analysing results

• New Shiny-based graphical interface functions:
• launchDiffExprLoader(): load differential expression data
• launchCMapDataLoader(): load CMap data
• launchResultPlotter(): view and plot data results
• launchMetadataViewer(): check metadata of a given object

Major changes

• downloadENCODEknockdownMetadata(): metadata is automatically saved to a file in order to avoid downloading metadata every time this function is run
• plotTargetingDrugsVSsimilarPerturbations():
• automatically look for matching compounds in multiple columns of both datasets
• allow to manually select columns on which to merge datasets
• prepareDrugSets(): drug sets based on numeric molecular descriptors are now prepared using evenly-distributed intervals

• Simplify tutorial

                    Changes in version 1.6.1                        
  

• listExpressionDrugSensitivityAssociation() lists available gene expression and drug sensitivity associations
• First argument of rankSimilarPerturbations() and predictTargetingDrugs() changed name from diffExprGenes to input and now accepts:
• Named numeric vector containing differential gene expression values with gene symbols as names, as before;
• Character vector containing a custom gene set to test for enrichment (only to use with GSEA).
• In rankSimilarPerturbations() and predictTargetingDrugs(), when performing gsea method, allow to set different gene set size for top up- and down-regulated genes with geneSize argument:
• e.g. geneSize=c(100, 200) creates gene sets from the top 100 up- and top 200 down-regulated genes
• using geneSize=c(150, 150) or geneSize=150 is equivalent
• Plotting:
• plot() now supports plotting predictTargetingDrugs() results for a given drug, e.g. plot(targetingDrugs, “1425”)
• plot() nows allows to set plot title with argument title
• plot() now plots results based on available methods instead of trying to plot based on results from spearman method only
• GSEA plots now support two or less gene hits
• GSEA plots now support plotting of multiple perturbations
• GESA plots now show the first and last values of ranked genes
• plotDrugSetEnrichment() now returns a list whose names are drug set names
• as.table() improvements:
• Return cell identifiers and gene information (if available and as needed)
• Support predictTargetingDrugs() results
• Return results ordered as found on input

Bug fixes and minor changes

• downloadENCODEknockdownMetadata() now correctly retrieves metadata following a change in the metadata content from ENCODE
• Fix bugs when rendering GSEA plots due to deprecated functions in ggplot2
• Improve tutorial
• Copy-edit CMap-related console messages
• Copy-edit function documentation

customCMPdb

             Changes in version 1.1.0 (2020-10-02)                  

• Initial version

             Changes in version 0.99.5 (2020-10-09)                 
  

• Addressed hard links in functions like “processDrugage”

             Changes in version 0.99.0 (2020-09-30)                 
  

• Consolidated two packages into one named as customCMPdb
• Supported customizing compound annotation database
• Add customized annotation table
• Delete
• List and set default
• Updated query interface
• Supported selecting annotation resources
• Supported querying added customized annotations

cytomapper

             Changes in version 1.1.6 (2020-10-23)                  

• Dropped 32-bit Windows support

             Changes in version 1.1.5 (2020-10-11)                  
  

• Prepared for Bioc 3.12 release

• Started unit testing the shiny app

             Changes in version 1.1.4 (2020-09-13)                  
  

• Allow channel-specific inputRange inputs for normalisation

             Changes in version 1.1.3 (2020-09-12)                  
  

• Extended vignette

• Changed package title

             Changes in version 1.1.2 (2020-07-17)                  
  

• Added shiny app to package

                    Changes in version 1.1.1                        
  

• Images are no longer re-normalized after channel merging (> 3 channels)

• Instead images are clipped at 1 leading to brighter colours

• The same happens for colour merging when colouring masks by feature expression

CytoML

                    Changes in version 3.11                         

API Changes

• Rename argument sampNLoc -> sample_names_from in open_flowjo_xml
• All parsers (flowjo/cytobank/diva_to_gatingset) now return GatingSet based on cytoset rather than ncdfFlowSet
• Add trans argument to cytobank_to_gatingset to allow overriding of transformations from gatingML file (#76)
• gatingset_to_flowjo now uses a docker image with a compiled converter: hub.docker.com/r/wjiang2/gs-to-flowjo
• Some updates to how flowjo_to_gatingset searches for FCS files (#77)
• Add include_empty_tree option to flowjo_to_gatingset to include samples without gates
• Allow gatingset_to_flowjo to take a path to a GatingSet archive directory
• Add gating_graphGML to replace gating.graphGML method for openCyto::gating generic
• Filter samples by panel when parsing cytobank experiment and add ce_get_samples, ce_get_panels

Fixes/internal changes

• Automatic time scaling of samples from FlowJo workspaces now handled by flowjo_to_gatingset RGLab/cytolib#33
• Handle change to default stringsAsFactors=FALSE in R 4.0
• Eliminated extra intermediate files left in temp directory during workspace parsing
• Switch usage of GatingSetList to merge_gs_list
• Solve some Windows build issues
• Switch from experimental::filesystem to boost::filesystem in C++ FlowJo parser

• Add CytoML XSD to installation

                    Changes in version 3.10                         
  

API Changes

• Change handling of quad gates according to RGLab/cytolib#16

• Renaming of methods:

• openWorkspace -> open_diva_xml, open_flowjo_xml
• cytobankExperiment -> open_cytobank_experiment
• cytobank2GatingSet -> cytobank_to_gatingset
• parseWorkspace -> flowjo_to_gatingset, diva_to_gatingset
• getSampleGroups -> fj_ws_get_sample_groups, diva_get_sample_groups
• getSamples -> fj_ws_get_samples, diva_get_samples
• getKeywords -> fj_ws_get_keywords
• getCompensationMatrices -> ce_get_compensations
• getTransformation -> ce_get_transformations

• compare.counts -> gs_compare_cytobank_counts

• Renaming of classes:

• divaWorkspace -> diva_workspace

• flowJoWorkspace -> flowjo_workspace

• Add CytoML.par.set, CytoML.par.get for setting parameters in CytoML namespace

Fixes/internal changes

• Make gatingset_to_cytobank export cytobank ML with attribute namespaces
• Allow diva_to_gatingset to use compensation matrix from xml
• Pass … args from cytobank_to_gatingset appropriately down to FCS parser
• Fix some issues with scaling of gates parsed from Diva workspace (#64)
• Guard against unsupported transformations being added to GatingSet during Diva parsing
• Switch diva_to_gatingset to using flowjo_log_trans instead of logtGml2_trans
• Fix ported flowUtils::xmlTag to enable self-closing tags
• Make gating.graphGML lookup tailored gates by FCS name as well as file id
• Add some flexibility to getSpilloverMat used in gatingset_to_flowjo

CytoTree

             Changes in version 0.99.6 (2020-06-19)                 

• Remove INFO/WARNING/ERROR tags

• Add vignettes

             Changes in version 0.99.5 (2020-06-18)                 
  

• Re-build this package

             Changes in version 0.99.4 (2020-06-05)                 
  

• Change examples and provide use case

             Changes in version 0.99.3 (2020-06-02)                 
  

• Update for the comments from the reviewer

             Changes in version 0.99.2 (2020-05-24)                 
  

• Update R version to 4.0

             Changes in version 0.99.1 (2020-05-10)                 
  

• Fixed some warnings in BiocCheck

             Changes in version 0.99.0 (2020-05-10)                 
  

• First commit

dagLogo

                   Changes in version 1.27.9                        

• update the hyperlink of p.adjust.methods in documentation.

                   Changes in version 1.27.8                        
  

• add adjust p-value for testDAU function.

                   Changes in version 1.27.7                        
  

• optimize the label position of markers for logo.

                   Changes in version 1.27.6                        
  

• add markers for logo.

                   Changes in version 1.27.5                        
  

• allow multiple species for prepareProteome.

                   Changes in version 1.27.3                        
  

• fix the typo in dagLogo documentation.

                   Changes in version 1.27.2                        
  

• add availableSchemes function.

• fix the x-axis.

                   Changes in version 1.27.1                        
  

• adjust the Depends, Imports and Suggests packages

DAMEfinder

                    Changes in version 1.1.3                        

• Add CITATION

• Remove “bad chromosome” filtering

• Argument build in extract_bams() removed

                    Changes in version 1.1.2                        
  

• Remove vcfR dependency and add VariantAnnotation

                    Changes in version 1.1.1                        
  

• Fix typo in split_bams that excluded some chromosomes

dasper

                   Changes in version 0.99.2                        

NEW FEATURES

• Merge documentation into one man page for junction, coverage and outlier processing functions to reduce runtime of roxygen examples.

                   Changes in version 0.99.1                        
  

NEW FEATURES

• Change outlier_detect() to using basilisk for interfacing into python replacing reticulate.

                   Changes in version 0.99.0                        
  

NEW FEATURES

• Converted dasper into a Bioconductor-friendly format using biocthis.
• Added junction_load(), which loads raw junction data from RNA-sequencing into an RangedSummarizedExperiment object. Includes an option to allow download of user-specified control junctions.
• Added junction_annot(), which uses information from reference annotation and the strand of a junction to classify junctions as “annotated”, “novel_acceptor”, “novel_donor”, “novel_exon_skip”, “novel_combo”, “ambig_gene” and “unannotated”.
• Added junction_filter(), which filters junctions by their count, width, annotation or if they overlap a set of user-defined regions.
• Added junction_norm(), which normalises raw junction counts (into a proportion-spliced-in) by dividing the counts of each junction by the total number of counts in it’s associated cluster.
• Added junction_process(), a wrapper function for all “junction_” prefixed functions except junction_load().
• Added junction_score(), which scores patient junctions based on the extent their counts deviate from a control count distribution.
• Added coverage_norm(), which will load and normalise coverage for exonic/intronic regions corresponding to each junction.
• Added coverage_score(), which scores coverage associated with each junction based on it’s deviation from control coverage distributions.
• Added coverage_process(), a wrapper function for all “coverage_” prefixed functions.
• Added outlier_detect(), which uses the junction scores and coverage scores as input into an unsupervised outlier detection algorithm to find the most outlier-looking junctions in each sample.
• Added outlier_aggregate(), which aggregates the junction-level outlier data to a cluster-level.
• Added outlier_process(), a wrapper function for all “outlier_” prefixed functions.
• Added plot_sashimi(), which enables the visualisation of junction data across genes/transcripts or regions of interest.

decompTumor2Sig

             Changes in version 2.4.1 (2020-07-27)                  

• Removed dependency of package CRAN vcfR (archived on 2020-07-05), using functions of Bioconductor package VariantAnnotation instead

• Improved the mutation filtering so that multiallelic SNVs aren’t excluded when loading tumor genomes from a VCF file

• Updated citation and affiliation information

• Added consistency check for reference genome and genome annotation

• Improved error messages

deepSNV

             Changes in version 1.99.3 (2013-07-25)                 

Updates

• A few changes to shearwater vignette

• Renamed arguments pi.gene and pi.backgr in makePrior()

Bugfixes

• Fixed bug in bf2Vcf() when no variant is called

             Changes in version 1.99.2 (2013-07-11)                 
  

Updates

• Updated CITATION

• Added verbose option to bam2R to suppress output

• Changed mode() to “integer” for value of loadAllData()

Bugfixes

• Fixed bug when only one variant is called in bf2Vcf()

             Changes in version 1.99.1 (2013-06-25)                 
  

Updates

• Using knitr for prettier vignettes

• Including shearwater vignette

Bugfixes

• fixed issues with deletions in bf2Vcf()

• makePrior() adds background on all sites

             Changes in version 1.99.0 (2013-04-30)                 
  

Updates

• New shearwater algorithm

• Including VCF output through summary(deepSNV, value=”VCF”)

DegNorm

                   Changes in version 0.99.13                       

• bug fix and version bump .

                   Changes in version 0.99.12                       
  

• version bump.

                   Changes in version 0.99.11                       
  

• fix a bug in plot_coverage function and make changes in color scheme.

                   Changes in version 0.99.10                       
  

• Made additional required changes from review

                   Changes in version 0.99.9                        
  

• Made most required changes from review

                   Changes in version 0.99.8                        
  

SUBMIT TO BIOCONDUCTOR FOR REVIEW

• Corrected warnings and errors

DEGreport

                   Changes in version 1.25.1                        

• Fix: load dplyr::n() to avoid error

DelayedArray

                   Changes in version 0.16.0                        

NEW FEATURES

• Added ‘as.sparse’ argument to read_block() (see ?read_block) and to AutoRealizationSink() (see ?AutoRealizationSink).

• SparseArraySeed objects now can hold dimnames. As a consequence read_block() now also propagates the dimnames to sparse blocks, not just to dense blocks.

• Matrix multiplication is now sparse-aware via sparseMatrices.

• Added is_sparse<- generic (with methods for HDF5Array/HDF5ArraySeed objects only, see ?HDF5Array in the HDF5Array package).

• Added viewportApply() and viewportReduce() to the blockApply() family.

• Added set_grid_context() for testing/debugging callback functions passed to blockApply() and family.

SIGNIFICANT USER-VISIBLE CHANGES

• Renamed first write_block() argument ‘x’ -> ‘sink’

• Renamed: RealizationSink() -> AutoRealizationSink() get/setRealizationBackend() -> get/setAutoRealizationBackend() blockGrid() -> defaultAutoGrid() row/colGrid() -> row/colAutoGrid()

• Improved support of sparse data:
  • Slightly more efficient coercion from SparseArraySeed to dgCMatrix/lgCMatrix (small speedup and memory footprint reduction). This provides a minor speedup to the sparse aware block-processed row/col summarization methods for DelayedMatrix objects when the object is sparse. (These methods are: row/colSums(), row/colMeans(), row/colMins(), row/colMaxs(), and row/colRanges(). The methods defined in DelayedMatrixStats are not sparse aware yet so are not affected.)
  • Made the following block-processed operations on DelayedArray objects sparse aware: anyNA(), which(), max(), min(), range(), sum(), prod(), any(), all(), and mean(). With a typical 50%-60% speedup when the DelayedArray object is sparse.
  • Implemented a bunch of methods to operate natively on SparseArraySeed objects. Their main purpose is to support the above i.e. to support block processed methods for DelayedArray objects like sum(), mean(), which(), etc… when the object is sparse. Note that more are needed to also support the sparse aware block-processed row/col summarization methods for DelayedMatrix objects so we can finally ditch the costly coercion from SparseArraySeed to dgCMatrix/lgCMatrix that they currently rely on.

• The utility functions for retrieving grid context for the current block/viewport should now be called with no argument (previously one needed to pass the current block to them). These functions are effectiveGrid(), currentBlockId(), and currentViewport().

• DelayedArray now depends on the MatrixGenerics package.

BUG FIXES

• Various fixes and improvements to block processing of sparse logical DelayedMatrix objects (e.g. DelayedMatrix object with a lgCMatrix seed from thr Matrix package).

• Fix extract_sparse_array() inefficiency on dgCMatrix and lgCMatrix objects.

• Switch matrix multiplication to bplapply2() from bpiterate() to fix error handling.

DelayedMatrixStats

                   Changes in version 1.12.0                        

• Dispatch to sparseMatrixStats for sparse seeds that do not have their own methods (<URL: https://github.com/PeteHaitch/DelayedMatrixStats/pull/65>).

• Fix center= handling for all affected functions (<URL: https://github.com/PeteHaitch/DelayedMatrixStats/pull/65>).

• DelayedMatrixStats now imports the generics from MatrixGenerics. Thanks to Aaron Lun resolving this (<URL: https://github.com/PeteHaitch/DelayedMatrixStats/pull/62>).

DeMixT

                    Changes in version 1.6.0                        

• MPI for parallel computing is avaliable under R 4.0.0 for linux and Mac OS platforms.

• Gene expression data of normal tissues (Lung, Prostate and Thyroid) from the GTEx study are included.

• Rename DeMixT_S1 function to DeMixT_DE.

densvis

             Changes in version 0.99.0 (2020-09-24)                 

• First version of the package.

DepecheR

             Changes in version 1.5.4 (2020-09-17)                  

• Correction of the information about the content of the output from depeche.

             Changes in version 1.5.3 (2020-07-02)                  
  

• Correcting the p-adjustments, so that it in fact uses Benjamini-Hochberg, and

• not the more conservative Hochberg, as default.

             Changes in version 1.5.2 (2020-06-05)                  
  

• Introducing samplingSubset in the depeche function

• Bug fixes in dOptPenalty

• Small text updates to main vinjette and examples, without code implications.

             Changes in version 1.5.1 (2020-05-18)                  
  

• Introduction of neighSmooth - a generalization of groupStatPlot.

• Bug fix and simplification of dOptPenalty termination criteria.

• Re-tidying of the code base.

DESeq2

                   Changes in version 1.30.0                        

• Major overhaul of dispersion estimation and GLM estimation functions from Constantin Ahlmann-Eltze, which will allow use of the glmGamPoi package from within DESeq2, in particular relevant for single-cell datasets. DESeq() can be directed to use glmGamPoi for dispersion and GLM fitting by specifying fitType=”glmGamPoi”. The glmGamPoi estimation is much faster than original DESeq2 estimation for single-cell datasets, e.g. for 30,000 cells, calling glmGamPoi was 13x faster than original DESeq2. In addition, the dispersion estimation is more accurate for genes with many small counts, as found in single-cell datasets. See glmGamPoi manuscript for details on methods, doi: 10.1101/2020.08.13.249623.

• Added integrateWithSingleCell(), written by Kwame Forbes, which directs user to a menu of single-cell datasets available on Bioconductor and downloads/loads the one chosen by the user for further analysis visualization. (Interactive only)

DEWSeq

             Changes in version 1.3.0 (2020-09-30)                  

• modified authors and description sections in DESCRIPTION

DIAlignR

                    Changes in version 1.1.5                        

• ananlyteFDR to limit features for multipeptide.

• Removed decoy from features.

• BugFix alignment if all intensities are zero.

• Fixed printed stats.

DiffBind

                     Changes in version 3.0                         

• This is a major release of DiffBind and the new version will be 3.0.

The main upgrade involves how the modelling and normalization are done. DiffBind now supports models and contrasts of arbitrary complexity using either/both DESeq2 or/and edgeR, as well as a myriad of normalization options.

NB:

The previous methods for modelling are maintained for backward compatibility, however they are not the default. To repeat earlier analyses, dba.contrast() must be called explicitly with design=FALSE. See ?DiffBind3 for more information.

The default mode for dba.count() is now to center around summits (resulting in 401bp intervals). To to avoid recentering around summits as was the previous default, set summits=FALSE (or to a more appropriate value).

Normalization options have been moved from dba.analyze() to the new interface function dba.normalize(). Any non-default normalization options must be specified using dba.normalize().

• Summary of Changes:

  • dba.analyze():

  • Automatic mode can start at any point, including from a sample sheet, and continue default analysis

  • Remove normalization options bSubControl, bFullLibrarySize, filter, and filterFun from dba.analyze(), now set in dba.normalize().

  • Add support to analyze using full model design formula.

  • Update DESeq2 analysis method.

  • Update edgeR analysis method.

  • Moved edgeR bTagwise parameter to $config option

  • Remove support for DESeq analysis method.

  • Add ability to retrieve DESeq2 or edgeR object

  • dba.contrast():

  • Add design parameter to set design formula

  • Add contrast parameter to specify contrast using variety of methods

  • Add reorderMeta parameter to set factor value order

  • Add bGetCoefficients parameter to get design coefficient names to use in contrasts

  • NEW: dba.normalize():

  • Support TMM, RLE, and Library size noramlization for both DESeq2 and edgeR

  • Support background bin normalization using csaw

  • Support offsets and loess fit normalization

  • Support spike-in normalization with combined or separate reference genomes

  • Support parallel factor normalization

  • bSubControl default depend on presence of Greylist

  • dba.count():

  • Change default to summits=250; to avoid recentering around summits,must set summits=FALSE

  • Default for bUseSummarizeOverlaps in dba.count is now TRUE

  • Automatically detect single-end/paired-end in dba.count

  • Automatically index unindexed bams in dba.count and dba.normalize

  • move bSubControl parameter

  • Default score is now new score DBA_SCORE_NORMALIZED

  • Add minCount parameter to dba.count(), default now 0 instead of 1

  • Filtering peak by read count thresholds only available in dba.count()

  • Fix bug in dba.count() with user-supplied peakset and summits=n

  • NEW: dba.blacklist():

  • Apply ENCODE blacklist

  • Automatically detect reference genome for blacklist

  • Apply Greylists

  • Generate Greylists from controls using GreyListChIP package

  • Plotting changes:

  • Add loess fit line to dba.plotMA()

  • Add ability in dba.plotMA() to plot aribitrary samples (without contrast).

  • Add mask parameter to dba.plotBox()

  • Support negative scores, eg Fold changes in report-based objects, to enable fold-change heatmaps.

  • Removed bCorPlot as a parameter to dba(), dba.count(), and dba.analyze(). Use config.

  • dba.show() / print changes:

  • Updated dba.show() and print() to deal with designs and different contrast types

  • Add ability to retrieve design formula in dba.show()

  • Removed bUsePval parameter in dba.show()

  • Added constant variable DBA_READS to access library sizes

  • Vignette and help pages:

  • Replace multi-factor analysis section

  • Add extensive normalization section

  • Add blacklist/greylist section.

  • Add pike-in and parallel normalization examples

  • Add DiffBind3 help page and vignette section with information on backward compatibility.

  • Update technical details sections

  • General updates to all sections

  • Add GenerateDataFiles.R to package

  • Various bugfixes and cosmetic changes.

Director

             Changes in version 1.15.1 (2020-10-04)                 

• Updated DESCRIPTION and NEWS formatting.

DiscoRhythm

             Changes in version 1.5.6 (2020-07-22)                  

• Visual change to screen plot (No longer apply alpha to “after”).

• Bug fixes.

distinct

                    Changes in version 1.0.3                        

• FC and log2-FC calculation added (via ‘log2_FC’ function);

• ‘top_results’ function edited to sort results by p-value and log2-FC.

                    Changes in version 1.0.1                        
  

• substantial speed-up in distinct_test (~7 times faster);

• parallel computing introduced;

• modelling of covariates introduced, via a design matrix;

• two new functions to visualize results: plot_cdfs and plot_densities.

dittoSeq

                     Changes in version 1.2                         

• Added 3 New Visualization Functions, dittoDotPlot(), dittoDimHex() & dittoScatterHex().

• Expanded SummarizedExperiment compatibility across the entire toolset.

• Added ComplexHeatmap integration to dittoHeatmap(), controlled by a new input, complex.

• Added Rasterization for improved image editor compatibility of complex plots. (See the dedicated section in the vignette for details.)

• Added labels.split.by input & do.contour, contour.color, and contour.linetype inputs to scatter/dim-plots.

• Added order input to scatter/dim-plots for control of plotting order.

• Added metas input for displaying such data with dittoHeatmap().

• Added adjustment input to meta(), which works exactly as in gene() (but this is not yet implemented within data grab of visualiation functions).

• Added adj.fxn input to meta() aand gene() for added control of how data might be adjusted (but this is not yet implemented within data grab of visualiation functions).

• Replaced (deprecated) highlight.genes input with highlight.features in dittoHeatmap().

• Replaced (deprecated) OUT.List input with list.out for all multi_* plotters.

DMCFB

                    Changes in version 1.3.1                        

New Features

• Parallel reading of data is added to readBismark-method.

Removed

• export.bed is removed due to warning. Will be modified and added in the next release.

DMCHMM

                   Changes in version 1.11.1                        

CHANGES

• Parallel reading is added to readBismark-method.

BUG FIX

• Some bugs are fixed in methHMMCMC-method to avoid creating infinity.

DOSE

                   Changes in version 3.15.4                        

• update setReadable and geneInCategory methods for compareClusterResult object (2020-10-12, Mon)

                   Changes in version 3.15.3                        
  

• allow passing additional parameters to fgsea (2020-10-09, Fri)
• https://github.com/YuLab-SMU/DOSE/pull/40
• add termsim and method slots to compareClusterResult, enrichRestul and gseaResult

• https://github.com/YuLab-SMU/DOSE/pull/39

                   Changes in version 3.15.2                        
  

• update NCG and DGN data (2020-10-09, Thu)

drawProteins

                    Changes in version 1.9.0                        

• Default addition of chain where it is absent.

DropletUtils

                   Changes in version 1.10.0                        

• Migrated downsampleMatrix() to scuttle with a re-export.

• Added features= to downsampleReads() for per-feature-set downsampling.

• Added matrix support for y= and ambient= in maximumAmbience().

• Added controlAmbience() for easy estimation of ambient contamination with control features.

• Added removeAmbience() function to remove the ambient solution from a count matrix, mostly for aesthetics.

• Report library index and feature type in output of read10xMolInfo().

• Support subsetting by library index/type in functions that use the molecule information file, such as swappedDrops() and chimericDrops().

• Added by.rank= option to estimateAmbience() and emptyDrops(), for estimation of the ambient profile by excluding barcodes with the largest totals.

• Added exclude.from= option to barcodeRanks(), to avoid problems with instability at low ranks for knee/inflection calculations (contributed by Stefano Mangiola).

• Minor bugfix in barcodeRanks() calculation of the knee point. Note that this affects the default choice of retain= in emptyDrops().

• Split off HTO ambience inferences into a separate inferAmbience() function.

• Added support for combinatorial barcodes in hashedDrops().

easyRNASeq

                   Changes in version 2.25.1                        

• Ported changes from 2.24.1

                   Changes in version 2.24.1                        
  

• Final documentation fix and removal of defunct RangedData unit tests.

EDASeq

                   Changes in version 2.23.1                        

• Removed coercion methods to CountDataSet following DESeq deprecation.

• Updated vignette to show how to use EDASeq with DESeq2.

edgeR

                   Changes in version 3.32.0                        

• cpm.default() and rpkm.default() now accept offset.

• scaleOffset() now accepts CompressedMatrix offset and accounts for norm.factors.

• Revise the lowess trend fitting in voomLmFit() to downweight genes with exact zeros and hence fewer df to estimate the variance.

• Add as.data.frame method for DGEList class.

• Change default choice for refColumn in calcNormFactors() with method=”TMMwsp”. The new method chooses the column with the largest sum of sqrt-counts.

• processAmplicons() can now accommodate data from newer screens that use a staggered primer design.

• Fixed a bug that diffSpliceDGE() accept more than one coef. It now gives a warning if more than one coef or contrast is supplied. It only uses the first.

                 Changes in version 3.30.2                        
  

• New function voomLmFit() that combines the limma voom-lmFit pipeline with loss of residual df due to zero counts as for glmQLFit(). The new function is more robust to zero counts than running voom() and lmFit() separately. The new function allows sample quality weights and intra-block correlations to be estimated it incorporates the functionality of duplicateCorrelation() and voomWithQualityWeights() as well.

• New function SE2DGEList() to convert a SummarizedExperiment object into a DGEList object.

• S3 methods for SummarizedExperiment objects are added to the following functions: aveLogCPM(), calcNormFactors(), cpm(), cpmByGroup(), estimateDisp(), filterByExpr(), glmFit(), glmQLFit(), plotMD(), plotMDS(), predFC(), rowsum(), rpkm(), rpkmByGroup() and sumTechReps().

• New cpm and rpkm methods for DGEGLM and DGELRT objects.

• New function effectiveLibSizes() to extract normalized library sizes from an edgeR data object or fitted model object.

• Add as.data.frame methods for DGEExact and DGELRT objects and remove the ‘optional’ argument from as.data.frame.TopTags().

• readBismark2DGE() now forces ‘files’ to be character vector.

• Add warning messages when filterByExpr() is used without specifying group or design.

• Add warning message when calcNormFactors() is applied to DGEList object containing an offset matrix.

• Rewrite User’s Guide Section 3.5 on Multilevel Experiments so that the code is valid regardless of the number of subjects in each disease group.

EnhancedVolcano

                     Changes in version 1.8                         

• added functionality to encircle variables of interest

• added option to remove arrowheads on connectors

• added option to rasterise images via ggrastr::geom_point_rast (Benjamin Ostendorf)

• changed axis.text.y = element_text(…, vjust = 1.0) to 0.5 (Benjamin Ostendorf)

ENmix

                   Changes in version 1.25.9                        

• bugfix, updated user manual

EnrichmentBrowser

                   Changes in version 2.20.0                        

• New function import to import results from differential expression analysis with limma, edgeR, and DESeq2

• New function showAvailableSpecies to list supported species for a gene set database of choice (GO, KEGG, MSigDB, Enrichr, …)

• New function showAvailableCollections to list provided gene set collections for a supported species of a gene set database of choice (GO, KEGG, MSigDB, Enrichr, …)

• Gene sets: obtaining and caching of gene sets for different gene ID types (new argument gene.id.types for function getGenesets)

• GO gene sets: filter by GO evidence codes (new argument evid for function getGenesets)

• Including NEAT among nbea methods

enrichplot

                    Changes in version 1.9.5                        

• fix wordcloud_i (2020-10-15, Thu)

• Remove similarity calculation from emapplot

                    Changes in version 1.9.4                        
  

• implement pairwise_termsim to calculate similarity of enriched terms (2020-10-09, Fri)
• https://github.com/YuLab-SMU/enrichplot/pull/67
• change parameters to be more consistent

• https://github.com/YuLab-SMU/enrichplot/pull/62

                    Changes in version 1.9.3                        
  

• add node_label_size parameter to adjust the size of node label in emapplot function (2020-09-18, Fri)

                    Changes in version 1.9.2                        
  

• add function emapplot_cluster (2020-09-01, Tue)

ensemblVEP

                   Changes in version 1.32.0                        

• add support for Ensembl release 100/101

epivizrServer

                   Changes in version 999.999                       

• This NEWS file is only a placeholder. The version 999.999 does not really exist. Please read the NEWS on Github: <URL: https://github.com/epiviz/epivizrServer>

escape

                   Changes in version 0.99.9                        

• Changing Seurat dependency, updated vignette

                   Changes in version 0.99.8                        
  

• Edited getSignificance ANOVA model call

                   Changes in version 0.99.7                        
  

• Edited getSignificance fit call to match documentation

                   Changes in version 0.99.6                        
  

• Edited match.args() in getSignificance

                   Changes in version 0.99.5                        
  

• Edited match.args() in getSignificance

                   Changes in version 0.99.4                        
  

• Added match.args() to getSignificance

• Changed stop() to message()

• Modified getSignficance to allow for ANOVA and T.test

                   Changes in version 0.99.3                        
  

• Updated link in description of getGeneSets.

                   Changes in version 0.99.2                        
  

• *Fixed a parenthesis, yeah a parenthesis. (In enrichIt() call I edited for 99.1)

                   Changes in version 0.99.1                        
  

• Removed parallel call in gsva() and added biocparallel

• Changed cores = 4 to cores = 2 in the vignette

                   Changes in version 0.99.0                        
  

• Preparing for bioconductor submission

ExperimentHub

                   Changes in version 1.15.0                        

BUG FIXES

• (1.15.2) Proxy message formatting

USER-VISIBLE CHANGES

• (1.15.4) less stringent internet check

• (1.15.3) Add link for github issue reporting

• (1.15.1) Add hubs@bioconductor.org email for help

ExperimentSubset

             Changes in version 0.99.0 (2020-10-02)                 

PRE-RELEASE

• Pre-release version of the ExperimentSubset package to be submitted to Bioconductor

ExploreModelMatrix

                    Changes in version 1.1.4                        

• Updated interface to make better use of screen space
• Expanded explanation of statistical concepts

FamAgg

                   Changes in version 1.17.1                        

• Fix issue #20 (binary trait drops names upon conversion).

famat

             Changes in version 0.99.9 (2020-10-26)                 

• Updated examples data

             Changes in version 0.99.8 (2020-10-24)                 
  

• Fixed unit tests

             Changes in version 0.99.7 (2020-10-19)                 
  

• Removed UniprotR package

             Changes in version 0.99.6 (2020-10-19)                 
  

• Updated Biocmanager, devel version

             Changes in version 0.99.5 (2020-10-19)                 
  

• Fixed unit tests

             Changes in version 0.99.4 (2020-10-16)                 
  

• Removed biomart package

             Changes in version 0.99.3 (2020-10-16)                 
  

• Updated NEWS file

             Changes in version 0.99.2 (2020-10-16)                 
  

• Changed loops by apply functions
• Updated datasets documentation

• Updated DESCRIPTION file

             Changes in version 0.99.1 (2020-10-01)                 
  

• Fixed testthat issues

             Changes in version 0.99.0 (2020-09-24)                 
  

• Updated version for Bioconductor submission

           Changes in version 0.0.0.9000 (2020-09-01)               
  

• creation of the package

FGNet

                    Changes in version 3.23                         

• Kegg-related functionalities have been removed.

fgsea

                   Changes in version 1.15.2                        

• Faster perturbate thanks to Nikolay Budin

• Cleaner P-value and error estimations

FilterFFPE

             Changes in version 0.99.3 (2020-10-08)                 

• Fix error in the algorithm under multiple threading

• Speed up the filtering process using minMapBase

             Changes in version 0.99.0 (2020-08-20)                 
  

• Submitted to Bioconductor

fishpond

                    Changes in version 1.6.0                        

• Added makeInfReps() to create pseudo-inferential replicates via negative binomial simulation from mean and variance matrices. Note: the mean and the variance provide the inferential distribution per element of the count matrix. See preprint for details, doi: 10.1101/2020.07.06.189639.

• Added splitSwish() and addStatsFromCSV(), which can be used to distribute running of Swish across a number of jobs managed by Snakemake. See vignette for description of a suggested workflow. For a large single-cell dataset with mean and variance summaries of inferential uncertainty, splitSwish() avoids generating the inferential replicate counts until the data has been split into smaller pieces and sent to different jobs, then only the necessary summary statistics are gathered and q-values computed by addStatsFromCSV().

• plotInfReps() gains many new features to facilitate plotting of inferential count distributions for single cells, as quantified with alevin and imported with tximport. E.g. allow for numeric x argument plus grouping with cov for showing counts over pseudotime across groups of cells. Also added applySF argument which can be used to divide out a size factor, and the reorder argument which will re-order the samples/cells within groups by the count. plotInfReps() will draw boxplots with progressively thinner visual features as the number of cells grows to make the plots still legible.

                    Changes in version 1.5.2                        
  

• First version of makeInfReps(), to create pseudo-infReps via negative binomial simulation from set of mean and variance matrices in the assays of the SummarizedExperiment.

flowCut

                    Changes in version 1.0.0                        

NEW FEATURES

• (v. 0.99.0) This is the submitted version of the package.
• (v. 0.99.6) Added many crashes to avoid crashes.
• (v. 0.99.7) Added vignette files.
• (v. 0.99.8) Added “Was the file run twice” in data table. Edited data file to be consistent with fixes from other versions. Manual pages updated.
• (v. 0.99.11) Added UseCairo parameter since docker requires no Cairo when creating the pngs.
• (v. 0.99.12) Added UnifTimeCheck parameter to allow the user to adjust the value.
• (v. 0.99.13) Changed default UseCairo to F. Added UseCairo and UnifTimeCheck parameter to second run code. Changed email.
• (v. 0.99.14) Added AlwaysClean parameter to allow for not skipping if nice. Also added to the man pages.
• (v. 0.99.16) Added IgnoreMonotonic paramater to ignore the monotonically increasing in time flagging test.
• (v. 0.99.17) Changed license.
• (v. 0.99.18) Added monotonic time fix option.

BUG FIXES

• (v 0.99.1) Small fixes from the bioconductor bot review process.
• (v 0.99.2) Review fixes.
• (v 0.99.9) Fixed a bug that occured if the first channel being cleaned was the first one. This only happens if there is not FSC or SSC channels.
• (v 0.99.10) Fixed bug where time tests fails on second run of flowCut
• (v 0.99.15) Small bug fix with monotonically increasing channels.
• (v 0.99.19) Fixed formatting issues in vignette.
• (v 0.99.20) Fixed formatting issues in vignette.
• (v 0.99.21) Fixed spacing issues.
• (v 0.99.22) changed 1: to seq_len
• (v 0.99.23) changed codes formatting
• (v 0.99.24) changed codes formatting
• (v 0.99.25) More formatting and code optimization edits, changed NEWS to NEWS.md
• (v 0.99.26) resolved installation issues
• (v 0.99.27) Small bug fix with monotonically increasing channels.

flowFP

                   Changes in version 1.47.0                        

• The update to R4.0.2 caused warnings like: Warning messages: 1: In .Call(“bin_level”, fcs@exprs, model@.tmp_tags, model@split_axis[[level]], : converting NULL pointer to R NULL. The c code was updated to avoid returning a null pointer.

• Updated citation syntax was incorporated in the CITATION file.

flowSpecs

             Changes in version 1.3.3 (2020-09-03)                  

• Changes to two tests due to minor errors

• Excluding the recommendation to use flowVS, due to its deprecation.

             Changes in version 1.3.2 (2020-05-15)                  
  

• Addition of peakNorm and associated test.

             Changes in version 1.3.1 (2020-05-15)                  
  

• Bug fix in arcTrans.

• Correcting the way specUnmix exchanges exprs objects.

fmrs

                   Changes in version 0.99.3                        

IMPROVEMENTS SINCE LAST RELEASE

• Compatibility with bioconductor is added.

                   Changes in version 0.99.0                        
  

• Package moved to bioconductor.

BUG FIXES

• Several bugs are fixed.

FRASER

                    Changes in version 1.1.6                        

• Use proper S3/S4 methods to share functions between packages

• Minor API changes due to S3/S4 changes (e.g fds -> object)

• Switch from psiSite to theta

• Improved documentation

• Minor bugfixes

                    Changes in version 1.1.3                        
  

• Update and adjust injectOutlier and hyperParameter functions

• Option to compute z scores in logit space or not

• Add cap value [0.01,0.99] to logit function

• Use pairedEnd counting with Rsubread

• Correct assayName pajd -> padj

• Minor bugfixes

                    Changes in version 1.1.2                        
  

• Option to consider only the standard chromosomes in the counting

• Option to include additional columns from mcols(fds) in the result table

• Annotation of junctions with corresponding gene names/ids now produces an additional column in mcols(fds) that contains further gene names/ids if the junction overlaps with multiple genes

• Minor bugfixes

                    Changes in version 1.1.1                        
  

• Bugfix correcting the strand specific counting for paired-end reads

FScanR

             Changes in version 0.99.7 (2020-09-08)                 

• ReSubmitted to Bioconductor

             Changes in version 0.99.6 (2020-08-27)                 
  

• ReSubmitted to Bioconductor

             Changes in version 0.99.5 (2020-08-27)                 
  

• ReSubmitted to Bioconductor

             Changes in version 0.99.4 (2020-08-27)                 
  

• ReSubmitted to Bioconductor o Remove duplicates of detected PRF events from output

             Changes in version 0.99.3 (2020-08-26)                 
  

• Submitted to Bioconductor

gage

                   Changes in version 2.39.3                        

• fixed warning on “library(GO.db)” in go.gsets.R. Now “import” from GO.db, instead of “suggest” it.

                   Changes in version 2.39.2                        
  

• fixed error caused by class(exprs) == “data.frame” in gagePrep.R. class(exprs) now returns a vector of length 2, which caused the error.

GAPGOM

             Changes in version 1.5.1 (2020-07-01)                  

Changed

• Added cre to new maintainer in description file.

GCSConnection

                    Changes in version 1.1.6                        

• add gcs_rm function

                    Changes in version 1.1.5                        
  

• Add gcloud into the default authentication process

                    Changes in version 1.1.4                        
  

• gcs_is_requester_pays supports uri

• Better print format in gcs_get_cloud_auth

                    Changes in version 1.1.3                        
  

• FileClass object can show the file URL now

• no warning will be given if gcs_dir find a non-standard file path

• Fix some word issues: all xxx_url functions are renamed to xxx_uri

                    Changes in version 1.1.2                        
  

• Support Requester Pays

• Support ~ symbol to go to the bucket root

• Support conversion from Folder/File class to character

gdsfmt

                   Changes in version 1.24.1                        

UTILITIES

• ‘show’ option in print.gds.class() for array preview

GENESIS

                   Changes in version 2.19.7                        

• Change default value of small.samp.correct in pcrelate to TRUE.

• Add options to remove NxN matrices from a null model (function nullModelSmall and fitNullModel argument return.small).

• Add check for collinearity in covariates.

                   Changes in version 2.19.6                        
  

• Add test options “BinomiRare” and “CMP” to assocTestSingle and assocTestAggregate.

                   Changes in version 2.19.5                        
  

• Add function jointScoreTest to perform a joint score test of a set of variants using a null model and a matrix of genotype dosages.

                   Changes in version 2.19.4                        
  

• Add function effectAllele to return the effect allele for association tests.

                   Changes in version 2.19.1                        
  

• Force design matrices to be non-sparse.

GeneTonic

                    Changes in version 1.2.0                        

New features

• The geneset distillery is officially open! GeneTonic offers functionality to aggregate together gene sets into overarching biological themes, based on a network-based refinement of the enrichment map. Corresponding graphical functionalities are also extended to accommodate meta-genesets. An efficient implementation for the Markov clustering on graph objects is also provided

• GeneTonic can now receive the input of many other tools for functional enrichment analysis - this includes the output (text export) of DAVID (shake_davidResult), enrichr (from website and via the package, with shake_enrichrResult), fgsea (shake_fgseaResult), and g:Profiler (with shake_gprofilerResult, which can handle the textual output from the website, as well the one from the call to the gost in gprofiler2)

• An export button to a SummarizedExperiment object for iSEE and its underlying machinery has been added. If the visualization options in GeneTonic are not exactly what you would expect, you might find an excellent venue in the iSEE framework

Other notes

• Added an additional mechanism for safe fails when not finding the GO Term and searching for the definition - this could happen e.g. when the term becomes outdated and is removed from the GO.db package, or also mistyped if entered by hand at some point.
• gs_heatmap has a new parameter, plot_title, to override the title to be displayed and set it to any custom string
• It is now possible to save a snapshot of the graphs created with visNetwork
• The Gene Box now also contains links to the GTEx portal for the selected feature
• export_to_sif enables to export a graph object to a text file, encoded with the SIF format

GenomeInfoDb

                   Changes in version 1.26.0                        

NEW FEATURES

• The seqlevelsStyle() getter and setter now support style “RefSeq” when the underlying genome is known.

• Register a bunch of new NCBI assemblies and UCSC genomes. Use registered_NCBI_assemblies() and registered_UCSC_genomes() to get the lists of supported NCBI assemblies and UCSC genomes.

SIGNIFICANT USER-VISIBLE CHANGES

• The seqlevelsStyle() getter and setter do a better job when the underlying genome is known. The new behaviors address two long-standing shortcomings of the old behaviors:
  • In general, the seqlevelsStyle() setter didn’t know how to rename the scaffolds in an object. Now it does.
  • Also, for some assemblies that use unconventional chromosome naming conventions (e.g. Macaca_fascicularis_5.0), the seqlevelsStyle() getter was not able to detect the naming style and the seqlevelsStyle() setter was not able to rename the chromosomes. Now they both do the right thing. These improvements address these shortcomings but only in the situation where the underlying genome is known e.g. when ‘unique(genome(x))’ is “macFas5” or “Macaca_fascicularis_5.0”. When the underlying genome is not known, nothing has changed.

DEPRECATED AND DEFUNCT

• Deprecate releaseName() method for GenomeDescription objects.

BUG FIXES

• Small fix to getChromInfoFromNCBI().

genomeIntervals

                   Changes in version 1.45.2                        

• Ported changes from 1.44.2

                   Changes in version 1.45.1                        
  

• Ported changes from 1.44.1

                   Changes in version 1.44.2                        
  

• Updated the maintainer email address

• Cleared the imports

                   Changes in version 1.44.1                        
  

• Updated the vignette (data.frame() default is not a factor anymore for character vectors in R4)

• Removed the defunct RangedData usage

GenomicFeatures

                   Changes in version 1.42.0                        

NEW FEATURES

• Implement a restricted seqinfo() setter for TxDb objects that supports altering only the seqlevels and/or genome of the object, but not its seqlengths or circularity flags. This is all we need to make the improved seqlevelsStyle() setter work on TxDb objects (see below).

SIGNIFICANT USER-VISIBLE CHANGES

• The seqlevelsStyle() getter and setter do a better job when the underlying genome is known. See NEWS file in the GenomeInfoDb package for more information.

GenomicOZone

                    Changes in version 1.3.1                        

• Fixed a bug of always using Enssembl US server to annotate the genes.

• Updated the description in the DESCRIPTION file.

• Updated the citations.

GenomicRanges

                   Changes in version 1.42.0                        

NEW FEATURES

• Add nearestKNeighbors() method for GenomicRanges derivatives.

• coverage() now supports ‘method=”naive”’. This is in addition to the already supported methods “sort” and “hash”. This new method is a slower version of the “hash” method that has the advantage of avoiding floating point artefacts in the no-coverage regions of the numeric-Rle object returned by coverage() when the weights are supplied as a numeric vector of type ‘double’. See “FLOATING POINT ARITHMETIC CAN BRING A SURPRISE” example in ‘?coverage’ in the IRanges package.

getDEE2

                   Changes in version 0.99.16                       

• Functions getDee2Metadata and queryDee2 are now called getDee2Metadata and queryDEE2 respectively to be consistent with the other functions.

• Fixed a bug with some samples that have a # in the name. Thanks to @uilnauyis for the suggestion.

• New function getDEE2_bundle to fetch entire project data from http://dee2.io/huge/

                   Changes in version 0.99.9                        
  

• New function se() which constructs SummarizedExperiment object

                    Changes in version 0.0.2                        
  

• Some slight change to the vignette

ggtree

                    Changes in version 2.3.7                        

• add label_pad() function to add padding characters to taxa labels (2020-10-09, Fri) - https://groups.google.com/g/bioc-ggtree/c/INJ0Nfkq3b0/m/lXefnfV5AQAJ

• add family parameter to geom_tiplab()

                    Changes in version 2.3.6                        
  

• new layouts, roundrect and ellipse
• https://github.com/YuLab-SMU/ggtree/pull/344
• https://github.com/YuLab-SMU/ggtree/pull/346
• fortify() method for treedataList object (2020-09-20, Sun)
• vexpand() and ggexpand() to expand plot limit by ratio of plot range (2020-09-18, Fri)
• geom_cladelab(), an updated version of geom_cladelabel that supports aes mapping (2020-09-17, Thu)

• https://github.com/YuLab-SMU/ggtree/pull/342

                    Changes in version 2.3.5                        
  

• td_unnest() which return a function to flatten ggtree plot data (2020-09-14, Mon)
• https://yulab-smu.top/treedata-book/chapter12.html#td_unnest
• update geom_hilight to support geom_hilight(data = mydata, node = selected_node) (2020-09-03, Thu)
• Defunct geom_nodelab2() (2020-09-02, Wed)
• geom_tiplab() and geom_nodelab() support geom = “shadowtext”
• td_filter() which return a function to subset ggtree plot data in geom layers (2020-08-29, Sat)
• https://yulab-smu.top/treedata-book/chapter12.html#td_filter
• update man files of geom_rootedge and geom_point2

• update geom_hilight to support geom_hilight(data = tbl_tree, node = selected_node). (2020-09-03, Thu)

                    Changes in version 2.3.4                        
  

• zoomClade and geom_zoom_clade to zoom in selected clade (2020-08-04, Tue)
• these two functions are wrapper function of ggforce::facet_zoom
• update facet_labeller according to the change of ggplot2 (2020-07-28, Tue)
• defunct set_hilight_legend as now geom_hilight supports aesthetic mapping and can generate legend automotically
• remove annotation_image, phylopic and subview as they were defunct for quite a long time. Users should refer to the ggimage package if they want to annotate tree with image or subplots.
• as_ylab parameter added in geom_tiplab(), which supports displaying tip labels as y-axis label and only works for rectangular and dendrogram layouts

• hexpand to expand x limits by ratio of x range and supports both direction (1 for rhs and -1 for lhs) (2020-07-27, Mon)

                    Changes in version 2.3.3                        
  

• add type parameter in geom_hilight, default is auto, optional rect to rectangular layer, encircle to encircle layer and comment original geom_hilight, and support subset in aesthetic. (2020-07-23, Thu)
• update geom_hilight to support aesthetic mapping (2020-07-22, Wed)
• update geom_taxalink to support aesthetic mapping (2020-07-20, Mon)

• layout_inward_circular for layout_circular() + scale_x_reverse() (2020-07-16, Thu)

                    Changes in version 2.3.2                        
  

• update geom_taxalink to support circular layout tree (2020-07-13, Mon).

                    Changes in version 2.3.1                        
  

• fortify method for pvclust object (2020-06-21, Mon)
• add dot parameters for color or size of geom_hilight and more detail messages of warnings for extendto. (2020-06-16, Tue)
• modified the angle of clade labels. Added horizontal parameter to control whether set clade labels to horizontal. When the parameter was set to FALSE, it will be useful for the layouts in coord_polar, such as circular, fan, radial. To better view the clade labels, their angles has been adjusted. (2020-06-15, Mon)
• bug fixed in getYcoord_scale_category (2020-05-13, Wed)

ggtreeExtra

                   Changes in version 0.99.0                        

the 0.99.0 or 0.99.x version mean I am submitting it to Bioconductor. (20200710, Fri)

• 0.99.1 change svg of dev to png, set the dpi to 300. (20200714, Tue)
• 0.99.2 geom_axis_text support the single column axis. (20200717, Fri)
• 0.99.3 support inward_circular tree and geom_axis_text was build by position_identityx. (20200724, Fri)
• 0.99.4 fix the constant of barplot bug. (2020-07-25, Sat)
• 0.99.5 better support the layer when x axis is reverse. (2020-07-29, Wed)
• 0.99.6 support adjusting the angle of geom_text. (2020-07-31, Fri)
• 0.99.7 revise stylistic comment of R code and examples. (2020-08-04, Tue)
• 0.99.8 change the formatting of code chunk. (2020-08-04, Tue)

0.99.9

• modified the color aesthetics for geom_boxplot and geom_violin. (2020-08-14, Fri)
• keep all column of data of tree when it merge with external data. (2020-08-14, Fri)

0.99.10

• add geom_ringline to create the grid line of external ring layers. (2020-08-21, Fri)
• the addbrink and other argument control the line of margin has been removed. (2020-08-21, Fri)
• add pseudo axis line in geom_axis_text. (2020-08-21, Fri)

0.99.11

• geom_axis_text and geom_ringline are removed. (2020-08-24, Mon)
• user can use axis.params=list(add.axis=TRUE) and grid.params=list(add.grid=TRUE) to add the axis and grid lines of external layers, respectively. (2020-08-24, Mon)

0.99.12

• add upper and lower grid lines of y. (2020-08-26, Wed)

0.99.13

• update the method of ggplot_add.layer_fruits, when the offset between different fruit_plot is different, will use each offset in each fruit_plot. (2020-08-31, Mon)

0.99.14

• update normxy to support dendrogram layout. (2020-09-02, Wed)

0.99.15

• add add.another.axis in geom_fruit to add another axis. (2020-09-04, Fri)
• update normxy to fix the bug when negative values are present. (2020-09-04, Fri)
• update ggplot_add method of geom_fruit to support the orientation which x axis of the external is from bottom to top, when layout is dendrogram. (2020-09-04, Fri)

0.99.16

• change add.axis in axis.params from TRUE or FALSE to x or y or xy. (2020-09-05, Sat)
• remove add.grid in grid.params and default of grid.params is NULL. (2020-09-07, Mon)
• update method of axis tick and remove nbreaks, the breaks will be calculate by pretty. (2020-09-07, Mon)
• use substitute to allow list of axis.params or grid.params has empty argument, eg grid.params=list(color=”black”,). (2020-09-07, Mon)

0.99.17

• change add.axis to axis in axis.params. (2020-09-08, Tue)

0.99.18

• add nbreak in axis.params of geom_fruit, it will be sent to n of pretty to generate the desired number of intervals of axis. (2020-09-08, Tue)

0.99.19

• modified the namespace, remove geom_vline, add geom_segment. (2020-09-11, Fri)

                    Changes in version 0.0.1                        
  

• add vignettes. (20200707, Tue)

                   Changes in version 0.0.0.9                       
  

• support add the axis text of extra layer of geom_fruit using geom_axis_text. (20200630, Tue)
• optimize normalization of extra layer data. (20200701, Wed)

• fixed bug: changed layer to layers. (20200703, Fri)

                   Changes in version 0.0.0.8                       
  

• support data of NULL in geom_fruit, and user can add data by %<+% of ggtree. (20200628, Sun)

                   Changes in version 0.0.0.7                       
  

• add geom_fruit_list to support add the same position for multi layers. (20200622, Mon)

                   Changes in version 0.0.0.6                       
  

• automatically detect the ‘position’. (20200612)

                   Changes in version 0.0.0.5                       
  

• change pratio parameter to pwidth and remove tippoint parameter.

• change geom_add function to geom_totree function. (20200610)

                   Changes in version 0.0.0.4                       
  

• support tip point for geom_star or geom_point

• support geom_boxplot and geom_violin (20200606)

                   Changes in version 0.0.0.3                       
  

• add marginal line, and when x is character, the new x normalized should be started with zero. (20200601)

                   Changes in version 0.0.0.2                       
  

• The distance between the panel and tree can be adjusted using the “offset”. The value of associate panel were normalized in the range of x of tree. The width can be adjusted using the “pratio”. The “offset” and “pratio” are the ratio related to tree. (20200529)

                   Changes in version 0.0.0.1                       
  

• first version to github (20200528)

Glimma

                    Changes in version 2.0.0                        

• Brand new backend and API with major changes

• Plots can now be embedded in html reports

• Plots can now be saved

• Data from gene annotation and counts can now be saved

• Added many plot customisation options in MDS plot

glmGamPoi

                     Changes in version 1.1                         

• Remove dual likelihood functions for overdispersion estimation. Instead merge functionality into conventional_***. This should cause no user facing changes, however should make it easier to maintain the package

• Make conventional_score_function_fast() more robust to extreme inputs. Avoid numerically imprecise subtractions and employ bounds based on series expansions for very small input

• If dispersion estimate quits because there is no maximum or all y are 0, return iterations = 0

• Add limits (1e-16 / 1e16) for nlminb estimates of the dispersion. This protects against errors due to NA’s in the conventional_likelihood_fast

• Automatically set ‘size_factors = FALSE’ for input with 0 or 1 row. This will change the estimated beta, but not the mu’s

• Rename gampoi_overdispersion_mle() -> overdispersion_mle()

• Store data in the object returned by glm_gp()

• Remove Y from the interface of residuals.glmGamPoi, because I can just get it directly from fit$data

• Add function test_de() that does a quasi-likelihood ratio test to detect differentially expressed genes

• Add functionality to make a pseudobulk test directly from test_de() by aggregating the data around one column

• In group-wise beta estimation, fall back to optimize() if the Newton method fails

• Change the default size factor estimation method from “poscounts” to “normed_sum” and provide an easy way to call scran::calculateSumFactors()

• New “global” mode for dispersion estimation

GNET2

                    Changes in version 1.5.5                        

• Add function for similarity scores between given labels for samples and the clustering in each predicted module.

                    Changes in version 1.5.2                        
  

• extract_edges() now returns an adjacency matrix for interations and their scores.

GOSemSim

                   Changes in version 2.15.2                        

• new site, https://yulab-smu.top/biomedical-knowledge-mining-book/ for documentation (2020-09-04, Fri)
• update vignette

• update data/gotbl

                   Changes in version 2.15.1                        
  

• bug fixed of IC method when input IDs contain invalid terms. (2020-07-25, Sat)

GPA

                    Changes in version 1.1.0                        

• Made the following significant changes

• Incorporate ShinyGPA developed by Emma Kortemeier as a part of the R package.

• Add fitAll() to fit GPA models for possible pairs of phenotypes.

• Add shinyGPA() to open the shiny app for the interactive pleiotropy visualization.

graphite

             Changes in version 1.35.2 (2020-10-12)                 

• Updated all pathway data.

GreyListChIP

                   Changes in version 1.22.0                        

• Add black lists for C. Elegans ce11, mouse dm6.

• Update existing black lists to version 2, or version 3 for human GRCh37, GRCh38.

GSEAmining

                   Changes in version 0.99.0                        

• Submitted to Bioconductor

GSgalgoR

             Changes in version 0.99.3 (2020-10-23)                 

• fix several issues acording to bioc revision

• add accessor functions to galgo.Obj object

             Changes in version 0.99.0 (2020-09-01)                 
  

• Remove gpuR support

• fix problem with small population

• Bioconductor Submission

             Changes in version 0.5.0 (2020-08-02)                  
  

• Rename to GSGalgoR

             Changes in version 0.4.2 (2020-07-21)                  
  

• Pre-release before Bioconductor submission

Gviz

                   Changes in version 1.33.1                        

NEW FEATURES

• score in sashimi plots can be transformed using function specified either in sashimiTransformation or transfromation (latter applied also to coverage)

BUG FIXES

• none

gwascat

                   Changes in version 2.21.7                        

USER VISIBLE CHANGES

• Oct 19 2020 – peculiar content in CHR_ID and CHR_POS cause truncation. Improved read_tsv call by setting col_types

                    Changes in version 2.21                         
  

USER VISIBLE CHANGES

• April 30 2020 – use BiocFileCache to manage retrieval from EBI

• May 2 2020 – ebicat_2020_04_30 is a sample of 50000 records from a full retrieval

• May 2 2020 – many data() elements moved to inst/legacy, LazyData turned off

GWASTools

                   Changes in version 1.35.2                        

• Replace read.table and write.table with much faster data.table::fread and data.table::fwrite in functions that convert to and from text. The exception is createAffyIntensityFile and checkIntensityFile(affy.inten=TRUE), which still use read.table to preserve the behavior of removing lines commented with the “#” character.

HCAMatrixBrowser

                    Changes in version 1.0.0                        

New features

• HCAMatrixBrowser finally on Bioconductor!
• HCAMatrixBrowser uses OpenAPI Specification version 2 and rapiclient to provide R API representations.
• loadHCAMatrix provides users with matrix data given a set of ‘bundle_fqids’
• Filtering on the main API object is supported see HCAMatrix for details
• Representations in all formats is supported this includes (.csv, .mtx, and .loom)
• Caching implemented using BiocFileCache
• MTX format support provided by Martin @mtmorgan
• Support for LOOM files provided by LoomExperiment
• CSV format files given as a tibble list

Bug fixes and minor improvements

• Updated vignettes to include API changes
• Allow for singleton bundle_fqid queries for v0 endpoint (@dvantwisk, #2)

HDF5Array

                   Changes in version 1.18.0                        

NEW FEATURES

• Add ‘as.sparse’ argument to h5mread(), HDF5Array(), HDF5ArraySeed(), writeHDF5Array(), saveHDF5SummarizedExperiment(), and HDF5RealizationSink(). Even though it won’t change how the data is stored in the HDF5 file (data will still be stored the usual dense way), the ‘as.sparse’ argument allows the user to control whether the HDF5 dataset should be considered sparse (and treated as such) or not. More precisely, when HDF5Array() is called with ‘as.sparse=TRUE’, the returned object will be considered sparse i.e. blocks in the object will be loaded as sparse objects during block processing. This should lead to less memory usage and hopefully overall better performance.

• Add is_sparse() setter for HDF5Array and HDF5ArraySeed objects.

SIGNIFICANT USER-VISIBLE CHANGES

• Change default value of ‘verbose’ argument from FALSE to NA for writeHDF5Array(), saveHDF5SummarizedExperiment(), and writeTENxMatrix().

BUG FIXES

• Fix handling of logical NAs in h5mread().

• Fix bug in saveHDF5SummarizedExperiment() when ‘chunkdim’ is specified.

Herper

             Changes in version 0.99.2 (2020-10-19)                 

• Updates for Bioconductor review

             Changes in version 0.99.0 (2020-09-17)                 
  

• Submitted to Bioconductor

HIBAG

                   Changes in version 1.26.0                        

• users can interrupt the model building in an interactive R session

• remove hlaErrMsg() since it is never used

• a new option ‘nthread’ in hlaAttrBagging() as a complement to hlaParallelAttrBagging()

• kernel version 1.5: generates the same training model as v1.4, but 2-6x faster, by taking advantage of Intel AVX, AVX2 and AVX512 intrinsics

• new function hlaSetKernelTarget() to automatically select the CPU target the algorithm is optimized for

HiCcompare

             Changes in version 1.11.1 (2020-08-14)                 

• Add CITATION, also to README.md file

• Update NEWS

• Update DESCRIPTION o Add Mikhail Dozmorov as Maintainer o Add URL and BugReports fields

• Revert breaking changes o KRnormalization.R, line 75, Z = rk/v; rho_km1 = t(rk) %*% Z; o hic_compare.R, line 99, A.min <- ceiling(mean(A_q10))

             Changes in version 1.11.0 (2020-02-11)                 
  

• New method to read in .cool files, cooler2bedpe()

• New method for comparison, hic_compare()

HPAStainR

             Changes in version 0.99.2 (2020-09-02)                 

• R code

• Changed high stringency to include Enhanced and Supported removing Approved

             Changes in version 0.99.1 (2020-08-06)                 
  

• Responded to comments from Bioconductor reviewer

• DESCRIPTION

• Moved tibble and shiny to imports

• Vignettes

• Made installation section

• Added table of contents

• Updated vignette text to agree with code

• Included sessionInfo()

• R code

• Updated HPA_data_downloader to fit bioconductor standards for accesing a website.

• Reduced number of lines >80

• Reduced number of indents not multiples of 4 spaces

             Changes in version 0.99.0 (2020-07-15)                 
  

• Package prepared for submission to Bioconductor

• Updated to coding practices

• No Biocheck Errors

• Updated imports and examples

hypeR

                   Changes in version 1.05.03                       

• rctbl_build() now wraps hyp objects into unlabled multihyp objects

• rctbl_build() nested tables shows the number of enriched genesets

                   Changes in version 1.05.02                       
  

• Correct file extensions (.rmd/.html) from output of hyp_to_rmd()

• Relative paths are now supported by hyp_to_rmd()

                   Changes in version 1.05.01                       
  

• Fixed bug for wrong column names from enrichr_available()

• Added the first shiny module for geneset selection

                   Changes in version 1.05.00                       
  

• Version bump for bioconductor
• Fixed hyp_dots(merge=TRUE) bug where some genesets were not showing
• Added support for fetching non-human Enrichr libraries (e.g. Yeast, Fly, Worm, Fish)
• Better reporting through rctbl_hyp() and rctbl_mhyp()

ideal

                   Changes in version 1.14.0                        

Other notes

• Replaced dependency from d3heatmap with the functionality of heatmaply

idr2d

                    Changes in version 1.2.2                        

• skipped Python-dependent tests on i386 systems (64-bit version of Python is required)

IgGeneUsage

             Changes in version 1.3.3 (2020-10-15)                  

• More flexible model for microbial sample analysis provided in inst folder, however, no interface is provided to it.

illuminaio

             Changes in version 0.31.1 (2020-07-15)                 

UPDATES

• Error messages produced by readIDAT() when failing decrypt no longer appends an extra newline at the end.

• readIDAT() uses explicit stringsAsFactors=FALSE internally.

• readIDAT() no longer keeps two file connections open at the same.

DOCUMENTATION

• The BibTeX URL reported by citation(package=”illuminaio”) was broken.

BUG FIXES

• readBGX() would leave an open connection if there was an file reading error.

             Changes in version 0.31.0 (2020-04-27)                 
  

NOTES

• The version number was bumped for the Bioconductor develop version, which is now BioC 3.12 for R (>= 4.0.0).

ILoReg

             Changes in version 0.99.0 (2020-06-25)                 

• The first version 0.99.0 is submitted to Bioconductor

immunoClust

                   Changes in version 1.21.2                        

• CHANGES
  • plot of no clusters
  • soves the deprecated warning from flowCore

  • code cleaning

                   Changes in version 1.21.1                        
    

• CHANGES
  • authors email contact

infercnv

             Changes in version 1.5.3 (2020-10-23)                  

• Add check that detectCores() doesn’t return NA before comparing. In case it does, just use the value provided as an option directly.

             Changes in version 1.5.2 (2020-10-23)                  
  

• Added reordering of cells in metadata exported to a seurat object so that it always matches, in case the cells are not sorted in the same order in the data provided to infercnv and in seurat.

             Changes in version 1.5.1 (2020-10-06)                  
  

• Fix to reload in cases where comparing NULL/NA.

• Fixed issue in denoising when trying to reload results from step 18 or 19.

• Fixed MCMC Diagnostic plots by adding diagnostic generation.

• Update included data objects to contain additional option slot, and prevent common name collisions.

• Fully rename data objects and name of the vars they provide.

• Fix reference plotting not having access to the actual subclustering information but that of the previous provided data object (that was renamed to avoid name collision by mistake like this one).

• Added checks in add_to_seurat methods that there are gains/losses found when taking the top hits.

• Added check that output to write in add_to_seurat top regions is not null and output an empty file without erroring if it is.

• Change to remove genes in “chr_exclude” from counts before doing the read level filtering of cells.

• Added minimum read count requirement per cell of 1 after removal of “chr_exclude” genes so that there are no divisions by 0 when normalizing.

• Changed default min_max_counts_per_cell to select cells with at least 100 counts by default.

• Fix to plotting for HMM coloring of heatmap when the full range of values are not present.

• Fix to plotting when no reference groups are used to not produce warnings.

Informeasure

             Changes in version 0.99.8 (2020-10-06)                 

• make changes

             Changes in version 0.99.7 (2020-10-06)                 
  

• make changes

             Changes in version 0.99.6 (2020-09-21)                 
  

• make changes

             Changes in version 0.99.5 (2020-09-20)                 
  

• Fix the the issue reported in the build report where used “1:lenght”” instead of “seq_len”

• Use “<-“ for assignment rather than “=”

• Fix indentation

             Changes in version 0.99.4 (2020-08-14)                 
  

• Fix the warning of unnecessary package calls

             Changes in version 0.99.3 (2020-08-14)                 
  

• Fix the warning of unnecessary package calls

             Changes in version 0.99.2 (2020-08-14)                 
  

• Fix the warning of unnecessary package calls

             Changes in version 0.99.1 (2020-08-13)                 
  

• Made the following significant changes

• Added Informeasure.Rproj into the .gitignore file

• Replaced Author/Maintainer with Authors@R in the DESCRIPTION file

• Added a NEWS file

• Added a .R file in tests/ directory

• Update R version dependency from 3.5.0 to 4.0

• Use TRUE/FALSE instead of T/F in PMI.plugin()

             Changes in version 0.99.0 (2020-08-09)                 
  

• Submitted to Bioconductor

intansv

                   Changes in version 1.29.0                        

Notes

• Fix build error on Windows and Mac.

IRanges

                   Changes in version 2.24.0                        

NEW FEATURES

• coverage() now supports ‘method=”naive”’. This is in addition to the already supported methods “sort” and “hash”. This new method is a slower version of the “hash” method that has the advantage of avoiding floating point artefacts in the no-coverage regions of the numeric-Rle object returned by coverage() when the weights are supplied as a numeric vector of type ‘double’. See “FLOATING POINT ARITHMETIC CAN BRING A SURPRISE” example in ‘?coverage’.

DEPRECATED AND DEFUNCT

• Removed RangedData class and anything related to RangedData objects.

BUG FIXES

• Fix bug in list element recycling.

ISAnalytics

            Changes in version 0.99.15 (2020-10-22)                 

• Minor fix in import_association_file file function: added multiple strings to be translated as NA

            Changes in version 0.99.14 (2020-10-21)                 
  

• Minor fixes in tests

            Changes in version 0.99.13 (2020-10-19)                 
  

NEW FEATURES

• Added analysis functions CIS_grubbs and cumulative_count_union

• Added plotting functions CIS_volcano_plot

            Changes in version 0.99.12 (2020-10-04)                 
  

NEW FEATURES

• Added analysis function sample_statistics

SIGNIFICANT USER-VISIBLE CHANGES

• aggregate_values_by_key has a simplified interface and supports multi-quantification matrices

MINOR CHANGES

• Updated vignettes

• import_parallel_Vispa2Matrices_interactive and import_parallel_Vispa2Matrices_auto now have an option to return a multi-quantification matrix directly after import instead of a list

            Changes in version 0.99.11 (2020-09-21)                 
  

NEW FEATURES

• Added analysis functions threshold_filter, top_integrations
• Added support for multi-quantification matrices in compute_abundance

MINOR FIXES

• Fixed bug in comparison_matrix that ignored custom column names

• Fixed issues in some documentation pages

            Changes in version 0.99.10 (2020-09-14)                 
  

ISanalytics is officially on bioconductor!

NEW FEATURES

• Added analysis functions comparison_matrix and separate_quant_matrices
• Added utility function as_sparse_matrix
• Added package logo

SIGNIFICANT USER-VISIBLE CHANGES

• Changed algorithm for compute_near_integrations
• Added support for multi-quantification matrices to remove_collisions
• Added usage of lifecycle badges in documentation: users can now see if a feature is experimental/maturing/stable etc

MINOR FIXES

• Added fix for import_single_Vispa2Matrix to remove non significant 0 values

             Changes in version 0.99.9 (2020-09-01)                 
  

NEW FEATURES

• Added functionality: aggregate functions
• Added vignette on aggregate functions
• Added recalibration functions
• Added first analysis function (compute_abundance)

SIGNIFICANT USER-VISIBLE CHANGES

• Dropped structure ISADataFrame: now the package only uses standard tibbles

• Modified package documentation

             Changes in version 0.99.8 (2020-08-12)                 
  

• Submitted to Bioconductor

iSEE

                   Changes in version 2.1.27                        

• Minor edits to the API documentation.

                   Changes in version 2.1.26                        
  

• Disable the import button on the dimnames modal when transmitter has not made a selection.

• Separate the maximum number of factor levels for colors from other applications.

                   Changes in version 2.1.25                        
  

• Support a named vector in the SearchColumns field of the Table subclasses.

                   Changes in version 2.1.24                        
  

• Enable custom saving of the application state via the new saveState= argument.

• Switch colormap getters to use an internal cache to avoid conflicts with user entries.

                   Changes in version 2.1.23                        
  

• ExperimentColorMap inherits from Annotated.

                   Changes in version 2.1.22                        
  

• Split and rename scripts for test setup.

                   Changes in version 2.1.21                        
  

• Minor fix to unit test.

                   Changes in version 2.1.20                        
  

• Export even more internal utilities for re-use in downstream packages.

• Minor fixes to the ComplexHeatmapPlot documentation.

                   Changes in version 2.1.19                        
  

• Export more internal utilities for re-use in downstream packages.
• Added a generic to define the selection effect UI.
• Fixes to the ComplexHeatmapPlot observers, most obviously for the assay choice.

• Fixes to the underlying reactive framework to avoid bugs due to unresponsiveness.

                   Changes in version 2.1.18                        
  

• Bugfix to properly support dynamic classes on landing page.

                   Changes in version 2.1.17                        
  

• .refineParameters() for FeatureAssayPlot, SampleAssayPlot protects the x-axis choice against absent metadata.

• CSS classes for each panel are now defined at app run-time, to make it easier to write landing pages without specifying initial= in iSEE().

                   Changes in version 2.1.16                        
  

• Bugfix for initialization of the ColorByFeatureDynamicSource UI element in ColumnDotPlots.

                   Changes in version 2.1.15                        
  

• Allow labelling of the medoid for each level of a discrete variable in a scatter-type DotPlot.

• Turned on validity checks during [[<- assignment into Panel classes.

                   Changes in version 2.1.14                        
  

• Right-aligned the help icon for individual panel tour.
• Added tooltip for mouseovers on DotPlot panels.

• Allowed custom annotation about selected table row to to be displayed in Table panels.

                   Changes in version 2.1.13                        
  

• Refactored the heatmap feature selection modal to be reusable for selecting rows or columns in other contexts.

                   Changes in version 2.1.12                        
  

• Added panel-specific tours via the .definePanelTour() generic.

• Generalized the HiddenColumns mechanism to all Table subclasses.

                   Changes in version 2.1.11                        
  

• Added HiddenColumns slot to hide columns in ColumnDataTables and RowDataTables.

                   Changes in version 2.1.10                        
  

• Avoided transmitting multiple selections for Tables when the number of columns change.
• Hid irrelevant UI elements for Table multiple selections.
• Generalized information about the number of selected rows/columns in each panel.

• Streamlined the .defineOutput signature.

                    Changes in version 2.1.9                        
  

• Improved documentation for generics and classes.
• Defined .exportOutput method for the ComplexHeatmapPlot class.
• Added missing documentation for slots and methods in the ComplexHeatmapPlot class.
• Enforced sensible defaults for the dynamic selection setting.

• Extract assays with dimnames for correct indexing.

                    Changes in version 2.1.8                        
  

• Fixed control of legend point size for continuous covariates.

• Extended control of legend point size for violin plots and Hinton plots.

                    Changes in version 2.1.7                        
  

• Added control of legend point size under the “Text” category of teh “Visual parameters” box.

                    Changes in version 2.1.6                        
  

• Fixed bug for sizeBy observers.

                    Changes in version 2.1.5                        
  

• Fixed initialization of panel size to current value when the “Organize panels” window is closed and re-opened.

• Fixed removal of last panel from the interface.

                    Changes in version 2.1.4                        
  

• Added progress bar when exporting panel outputs.

• Fixed missing section in createLandingPage() man page.

                    Changes in version 2.1.3                        
  

• Fixed handling of logical > 1 when processing the CustomRowsText slot in the ComplexHeatmapPlot constructor.

                    Changes in version 2.1.2                        
  

• Added a new vignette to describe panel links.
• Fixed documentation for *DynamicSource slots.
• Fixed reception of single selection from plot at initialization.

• Removed deprecated functionality.

                    Changes in version 2.1.1                        
  

• Added vignette documenting the use of out-of-memory matrices for big data.
• Added TENxPBMCData to Suggests:.

iSEEu

                    Changes in version 1.1.9                        

• Ensure that global parameters only affect panels during construction.

                    Changes in version 1.1.8                        
  

• Added the AggregatedDotPlot panel to show marker-based dot plots.

                    Changes in version 1.1.7                        
  

• Improved safety and correctness of the calculation of the number of DEGs.

                    Changes in version 1.1.6                        
  

• Version bump to trigger reinstallation with new iSEE class definitions.

                    Changes in version 1.1.5                        
  

• Added panel-specific tours for all panel classes via the .definePanelTour() generic.

                    Changes in version 1.1.4                        
  

• Generalized the DE-related globals to work as patterns rather directly specifying the acceptable names.

• Align DynamicMarkerTable’s treatment of getTableExtraFields() with the globals strategy.

                    Changes in version 1.1.3                        
  

• Overhauled handling of global parameters for greater consistency.
• Added the LogFCLogFCPlot to plot two DE comparisons against each other.

• Switched to KEGGREST to get the names of pathways.

                    Changes in version 1.1.2                        
  

• Replaced GeneSetTable with the more general FeatureSetTable. Improved handling of arbitrary feature sets.
• Renamed DifferentialStatisticsTable to the more appropriate DynamicMarkerTable. Support inclusion of extra fields from the rowData.

• Global parameters now only affect construction of MAPlots and VolcanoPlots.

                    Changes in version 1.1.1                        
  

• Improved documentation of the ReducedDimensionHexPlot methods.

IsoCorrectoR

                    Changes in version 1.6.2                        

• as response to a post from Am Zimmerman on the bioconductor support site (https://support.bioconductor.org/p/132345/), log-space factorials were used to calculate internal correction probabilities.

IsoformSwitchAnalyzeR

            Changes in version 1.11.11 (2020-10-13)                 

• Update type: minor.

• Fixed the mistake in importIsoformExpression() introduced in last updated

            Changes in version 1.11.10 (2020-10-13)                 
  

• Update type: minor.

• Update of importIsoformExpression() fix the import of countsFromAbundance

             Changes in version 1.11.9 (2020-10-12)                 
  

• Update type: Minor.

• More updates regarding namespace and dependencies

             Changes in version 1.11.8 (2020-10-09)                 
  

• Update type: Minor.

• Description update regarding to namespace

             Changes in version 1.11.7 (2020-09-30)                 
  

• Update type: Minor.

• Various documentation updates

• The plotting order of the sub-plots of switchPlot() was changed to avoid problems when having long isoform names.

• analyzeSignalP() was updated to be more robust at handling SignalP5 data where very few predictions were done.

             Changes in version 1.11.6 (2020-09-17)                 
  

• Update type: Minor.

• Updated namespace.

             Changes in version 1.11.5 (2020-09-14)                 
  

• Update type: Minor.

• Updated example code in importIsoformExpression()

• Updated namespace

             Changes in version 1.11.4 (2020-09-10)                 
  

• Update type: Medium.

• importRdata() was updated to give examples of sequence names when no overlap between fasta file and expression data was found.

• importRdata() was updated to try and rescue missing gene_name annoations (must likely due to novel transcripts) and split merged genes (a problem often occuring when doing transcript assembly with tools such as Cufflinks/StringTie).

• importRdata() and importCufflinksFiles() was udated with an option to print a guesstimate on the number of genes with differential isoform usage.

• isoformToGeneExp() and importGTF() was updated to look for the annotation problems fixed by importRdata() and give warnings if pressent.

• The example data (from individual files) was updated to include CDS.

• extractGeneExpression(), a function that extracts gene level counts/expression from a switchAnalyzeRlist was introduced.

• prepareSalmonFileDataFrame() and importSalmonData() was introduced. Jointly these functions enable import of Salmon data via tximeta thereby omitting the manual integration of annotation data (gtf/fasta)

• isoformSwitchAnalysisPart2() was updated to only do enrichment analysis if enough events were found.

• preFilter() was updated to apply the gene expression to both conditions instead of the average across all samples thereby better filtering out untrustworthy genes.

• extractSplicingGenomeWide() and extractConsequenceGenomeWide() was updated to handle missing values when calculating summary statistics.

• extractSplicingEnrichment(), extractSplicingEnrichmentComparison(), extractConsequenceEnrichment(), extractConsequenceEnrichmentComparison() was updated to use binom.test() instead of prop.test() as this test more apporpriate when analyzing smaller number of events.

• extractSplicingEnrichment() and extractSplicingEnrichmentComparison() was updated to have more easily interpretable descriptions.

• extractSwitchOverlap() was updated to also plot overlap in isoform switches and now allows for control of which venn diagrams to make.

• switchPlot() was updated to only consider the dIFcutoff when classifying the “increased/decrease/unchanged usage”.

• switchPlotGeneExp(), switchPlotIsoExp(), switchPlotIsoUsage() and switchPlotTranscript() was updated to enable return of the ggplot2 object (instead of printing it)

• all extractConsequence() and extractSplicing() functions was updated to enable return of the ggplot2 object (instead of printing it)

• switchPlotTopSwitches() was updated to also have the onlySigIsoforms argument.

• Various documentation updates.

             Changes in version 1.11.3 (2020-05-20)                 
  

• Update type: Minor.

• importRdata was updated to handle GTF files with a lot of additional information.

• analyzeSignalP and analyzePFAM was updated to fix a problem with handling multiple files.

• analyzePFAM was updated to attempt to handle both fixed width files and broken fixed width files.

• isoformSwitchTestDEXSeq() and isoformSwitchTestDRIMSeq() was updated with the “keepIsoformInAllConditions” argument which allows data for an isoform to be kept in all comparisons even if it is only deemed significant in one comparison. TRUE by default.

• importCufflinksData() was updated to handle when pathToSplicingAnalysis was not used.

             Changes in version 1.11.2 (2020-05-12)                 
  

• Update type: Minor.

• A bug was corrected in extractSequence() which caused an error: “object ‘filterShortAALength’ not found”.

• In extractSequence() the minimul length kept when using the “removeShortAAseq” argument was raised to 11 amino acids to match the pfam website.

• An error in importRdata was fixed to re-enable removal of isoforms only found in annotation.

             Changes in version 1.11.1 (2020-05-05)                 
  

• (Version bump due to Bioconductor release).

• Update type: Minor.

• Update of code comments in importRdata()

• Update of printed message in importIsoformExpression()

• Update of analyzePFAM() to enable more robust import of fwf files with and without headers included. It also handles the mistake in pfam files with regards to the fixed width of files when the “coiled-coil” type are included.

isomiRs

                   Changes in version 1.17.2                        

FIX

• Fix n() error from dplyr. Now importing in NAMESPACE.

                   Changes in version 1.17.1                        
  

FIX

• Fix error in tibble when selecting a column. Now it needs unlist to coarce to a vector.

KEGGprofile

                   Changes in version 1.31.1                        

• Fix bugs in genes_kept to deal with NA in data

LACE

                    Changes in version 1.0.1                        

• From Travis-CI to Github Actions.

lefser

                    Changes in version 1.0.0                        

• lefser is the R implementation to the LEfSE method for microbiome marker discovery.
• It uses the Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis to find biomarkers in groups and sub-group blocks.
• See the method paper here: https://doi.org/10.1186/gb-2011-12-6-r60

limma

                   Changes in version 3.46.0                        

New functionality

• Add new function chooseLowessSpan().

• fitFDist() with a non-NULL covariate now fits a smoother trend (with fewer spline knots) than before unless there are at least 30 observations. This also affects squeezeVar() and eBayes() with trend=TRUE.

• Add new argument output.style to weightedLowess().

• write.fit() now outputs a blank column heading for the row names so that the number of column names in the delimited output file will agree with the number of columns (similar to write.csv in the base package).

Code improvements

• Subsetting and contrasts.fit() now work on MArrayLM objects even if the cov.coefficients component is absent.

• volcanoplot() now prompts user to run eBayes() if the object doesn’t contain p-values.

• Add checks and more informative error messages to getEAWP() and lmFit() when the data object is missing, NULL or has zero rows.

• Subsetting for RGList, MAList, EListRaw, EList, MArrayLM or TestResults objects now accepts arguments other than i or j but ignores them without an error. This is relevant if a user adds a drop argument by analogy with matrix subsetting. Previously that produced an error.

• Subsetting of TestResults now requires two arguments, same as all of the other data object classes listed above. Previously single index subsetting (for example object[i]) was allowed.

• Improved treatment of zero weights by weighted.median().

• More consistent use of rep.int(), rep_len() and rep() throughout the package.

• Replace NA with NA_real_ where appropriate.

• Add a message to topTableF() to warn that the function is obsolete and will be removed in a future version of limma. Remove usages of topTableF() from the User’s Guide.

• Remove obsolete function toptable(), which has been officially deprecated in favor of topTable() since 1 Feb 2018.

Documentation

• Revise and expand the weightedLowess help page.

• Add more explanation about “heirarchical” method in the details section of the decideTests() help page.

• Add Note to voom help page to emphasise that voom is not an appropriate tool to analyse expresssion measures that have been normalized for library size.

• Revise the help page for plotMDS() to clarify that the function can produce PCA plots as well as PCoA plots.

• Add example to EList-class help page.

• Edits to the eBayes help page.

• Edit concept entries for help files (for reference manual index).

Bug fixes

• Revise write.fit() so that column names of the output file are correct when digits=NULL and the fit object contains only one coefficient column. Previously the same contrast name was repeated as the column name for the coefficients, t-statistics and p.values, making them hard to distinguish.

• Bug fix to arrayWeights() when y contains NAs, the design matrix has several columns and some but not all genes have no residual df.

lipidr

                     Changes in version 2.4                         

• Added imputation function for untargeted lipidomics datasets

• Added function to boxplot enriched lipidsets related to chain length and unsaturation

LRBaseDbi

                    Changes in version 2.0.0                        

• pkgtitle and pkgdescription options were added in makeLRBasePackages

Maaslin2

                    Changes in version 1.3.2                        

• Resolve issue with x labels missing from boxplots for metadata variables without levels and increase max jpgs written.

• Update the check for variables with more than two levels that will require a reference provided by the user for the model and the boxplots to be more strict (ignore UNK in the level count, don’t check if it is a factor, and check to see if all of the levels are numeric to ignore continuous variables).

• Fix ZINB error.

                    Changes in version 1.3.1                        
  

• Add random effects capability to all the other non-LM models.

• Add variance filtering option with default set to 0.

• Normalization is now performed after filtering and N.not.zero is calculated on the untransformed space. Also includes minor edits to synchronize with the manuscript.

• Add reference option required for fixed effects variables with more than two levels. Reference used in model and for boxplots.

• Update heatmap to include all categorical levels.

maftools

                    Changes in version 3.12                         

BUG REPORTS

• Incorrect deduplication cases while validating MAFs. Issue: 623
• Fix repeated domain labels in lollipopPlot2. Issue: 614
• Fix Copy number labels and coloring in coBarPlot. Issue: 609
• Fix coloring issues for annotations in oncoplot in R < 4.0. Issue: 599

ENHANCEMENTS

• Updated TCGA TMB. All variants from MC3 results are restricted and harmonized to Agilent 35.8 MB capture kit. See ?tcgaCompare for details. Issue: 612
• Added SIMC1 protein to domain database. Issue: 616
• Added sampleOrder1 and sampleOrder2 arguments to coOncoplot. Issue: 592
• Added gene_mar outer_mar argument to coOncoplot. Issue: 260
• Added sample size warning messages to mafCompare. Issue: 602
• Added cohortFontSize and axisFontSize to tcgaCompare

NEW FUNCTIONS

• Added filterMaf function.

DEPRECATED

• signatureEnrichment will be deprecated in future. Currently kept for legacy purpose with a warning message. Issue: 607 615

MAGeCKFlute

                    Changes in version 1.9.1                        

• Turn off the Depmap analysis in vignettes because it’s time consuming

• Use count in EnrichedView when NES is not available

                    Changes in version 1.8.1                        
  

• Update the standard gene names

• Debug the color issue in the ScatterView

• Remove the usage of scale_color_npg and data.table::melt from the DensitiView

• Remove nPerm parameter from the enrich.GSE

• Download GO-gene relationship from NCBI ftp folder

• Move multiple imports to suggests

• Replace view_allpath with pathview.top in FluteMLE to allow users to set the number of pathways for pathview visualization.

marr

                   Changes in version 0.99.4                        

• code indentation updated.

• Renamed the class and constructor from marr to Marr on October 23, 2020.

                   Changes in version 0.99.3                        
  

• Bioconductor single package building error

                   Changes in version 0.99.2                        
  

• Expanded Description and changed the binwidth parameter in histograms on October 16, 2020.

                   Changes in version 0.99.1                        
  

• Added Authors@R to the description file.

                   Changes in version 0.99.0                        
  

• Submitted marr 0.99.0 to Bioconductor on October 2, 2020.

MatrixGenerics

                    Changes in version 1.2.0                        

• Add drop and type to generic signature of [row|col]Quantiles (<URL: https://github.com/Bioconductor/MatrixGenerics/pull/14>).

• Sync API with matrixStats v0.57.0 (<URL: https://github.com/Bioconductor/MatrixGenerics/issues/17>).

• Add default methods with user-friendly fallback mechanism (<URL: https://github.com/Bioconductor/MatrixGenerics/pull/16>). Suggested packages are now loaded the first time a MatrixGenerics’ generic is called (e.g. the first time MatrixGenerics::colVars() is called). With this new approach, if the user passes a dgCMatrix object and if sparseMatrixStats is already loaded, will ‘just work’ and the fallback mechanism won’t try to load anything.

• Dispatch on methods for matrix objects when table objects are supplied (<URL: https://github.com/Bioconductor/MatrixGenerics/pull/15>)

matter

                   Changes in version 1.15.1                        

BUG FIXES

• Remove ‘…’ from ‘which()’

megadepth

                   Changes in version 0.99.0                        

NEW FEATURES

• Added a NEWS.md file to track changes to the package.
• Documentation website is now available at http://LieberInstitute.github.io/megadepth/. It gets updated with every commit on the master branch (bioc-devel) using GitHub Actions and pkgdown.

MesKit

                   Changes in version 0.99.11                       

Changes

• Preparations for Bioconductor release 4.0.

• Bugfixes:
  • Fix ‘plotCNA’ to not show ‘chrSilent’.
• Other changes:
  • Update exmaples.

  • Removed useless datasets.

             Changes in version 0.99.0 (2019-06-01)                 
    

Changes

• Package created.

metabCombiner

             Changes in version 0.99.0 (2020-09-11)                 

• Submitted to Bioconductor

metabolomicsWorkbenchR

                   Changes in version 0.99.0                        

• Bioconductor submission

metaMS

                   Changes in version 1.25.1                        

• Unit Test bug fix

                   Changes in version 1.25.0                        
  

• NEW function SearchNIST added (Only Windows OS)

MetaNeighbor

                    Changes in version 1.9.1                        

• Add several parameters to control fast version of MetaNeighbor and MetaNeighborUS

• Add function to pre-train MetaNeighbor models.

• Add preprocessing function to merge SingleCellExperiment objects.

• Add utility functions related to meta-clusters, cluster graphs and visualization.

metaseqR2

             Changes in version 1.1.21 (2020-08-05)                 

NEW FEATURES

• Creation of UCSC track and assembly hubs through the provision of a FASTA genome and/or assembly file for a non-supported or custom organism.

BUG FIXES

• Fixed a problem with rownames when importing an existing counts table.

             Changes in version 1.1.19 (2020-07-29)                 
  

NEW FEATURES

• None

BUG FIXES

• Fixed several problems with respect to custom GTF annotation import, especially when the GTF is compliant with minor GTF standards.

• Fixed a few warnings resulting in errors in R>4.0.

             Changes in version 1.1.18 (2020-07-03)                 
  

NEW FEATURES

• Simple quantification, QC and reporting is now allowed without having to define a contrast or statistical tests to be performed.

• In case of only a contrast is defined but no statistical tests required only fold changes are calculated.

BUG FIXES

• Fixed undefined class/function leftovers from NOISeq integration.

             Changes in version 1.1.17 (2020-06-29)                 
  

NEW FEATURES

• Integrated functionalities from deprecated packages DESeq and NOISeq in order to maintain PANDORA

BUG FIXES

• Fixed report crash with the new readTargets wrapper function.

             Changes in version 1.1.16 (2020-06-22)                 
  

NEW FEATURES

• Added support for reading targets in YAML

BUG FIXES

• Fixed “rnacomp” plot trying to import to JSON db while not run.

• Fixed report crash when “exportWhere” was NA.

• Other minor bug fixes

             Changes in version 1.1.15 (2020-06-12)                 
  

NEW FEATURES

• Allow simple differential exon analysis

BUG FIXES

• Fixed annotation breaks from UCSC (rn, danRer).

• Fixed crash when using excludeList (due to attributes being gone after list subsetting).

             Changes in version 1.1.13 (2020-05-25)                 
  

NEW FEATURES

• Addition of the harmonic mean p-value combination method (Wilson, 2019 - https://doi.org/10.1073/pnas.1814092116)

• Addition of a new dataset (hg19pvalues) containing a set of gene p-values from Giakountis et al., https://doi.org/10.1016/j.celrep.2016.05.038 to be used in the main vignette as well as a playground for p-value combination

BUG FIXES

• Major bug fix! The order of p-values returned by statDss was inconsistent with the rest of the stat* functions.

• Other minor bug fixes.

MetCirc

             Changes in version 1.19.0 (2020-07-02)                 

• adapt to changes in MSnbase (renaming of Spectra to MSpectra)

MethReg

                    Changes in version 0.1.0                        

• Added a NEWS.md file to track changes to the package.

methrix

                   Changes in version 1.4.00                        

• read_bedgraphs() supports bedgraphs files from “Bismark_cov”, “MethylDackel”, “MethylcTools”, “BisSNP”, “BSseeker2_CGmap”

• write_bedgraphs() supports output to multiBed and metilene file formats

• write_bigwigs() exports methrix object as bigWigs

                   Changes in version 1.2.10                        
  

• BSgenome ref build parsing error. Issue: #24

• Show which CpGs are missing when loading bedGraphs. Issue: #22

• Faster HDF5 processing. PR: #21

• include SeqStyle option in Manual write_bedgraphs() function. PE: #20

• added the argument for SeqlevelsStyle and trackline in bedgraph. PR: #19

methylKit

                   Changes in version 1.15.3                        

NEW FUNCTIONS AND FEATURES

• add verbosity argument to methCall to allow for complete silencing of output, this will be set by processBismarkAln which gained ‘verbose’ argument

IMPROVEMENTS AND BUG FIXES

• update R requirement to (>= 3.5.0)

• processBismarkAln:
  • add verbose argument
  • update tests
  • update docs
• joinsegmentneighbours:
  • Catch case when only one groups is there
• regionCounts:
  • update docs: mention that the output will be sorted by default
  • Fixes #195
• vignette:
  • add faq paragraph about regionCount to the vignette explaining why we order input region
  • update paragraph about methyldackel when to use it instead of processBismarkAln
  • Fixes #162

• add extensive test for bedgraph export

• update and export tests for getMethylationStats

• add extensive tests for getCoverageStats

• add extensive tests for normalizCoverage

• update checks for dataSim:
  • if sample ids given check if length(sample.ids) == # replicates

• update tests for getMethylDiff

• unite destranding:
  • make sure high numbers are not used in scientific notation
  • fixes #129
  • switch to data.table based destranding as it is faster and more memory efficient for larger number of regions
• methseg:
  • catch error when joined segments produce only single range
  • Fixes #195
• calculateDiffmeth:
  • check if output is equal for memory and tabix file

  • Fixes #189

                   Changes in version 1.15.2                        
    

IMPROVEMENTS AND BUG FIXES

• check.dbdir: catch if path equals root (“/”) dir

• methRead:

  • add missing context argument for call to .procBismarkCytosineReport
  • fixes https://github.com/al2na/methylKit/issues/198

microbiome

             Changes in version 2.1.2 (2020-07-01)                  

• Core heatmap labeling improved

• aggregate_top_taxa deprecated

• bimodality and potential_analysis functions fixed

             Changes in version 2.1.1 (2020-04-06)                  
  

• Added overlap function

microbiomeExplorer

                    Changes in version 1.0.0                        

• Release

MicrobiotaProcess

                   Changes in version 1.1.13                        

• removed retrieve_seq and mapply_retrieve_seq function, since these need internet. Which might cause time out when check. (2020-10-16, Fri)

                   Changes in version 1.1.12                        
  

• modified a bug in diff_analysis.phyloseq: change tax_table(ps) to ps@tax_table to avoid generate error when tax_table is NULL. (2020-10-15, Thu)

                   Changes in version 1.1.11                        
  

• update the examples of drop_taxa. (2020-10-14, Wed)

                   Changes in version 1.1.10                        
  

• update ggdiffclade to support data.frame input when reduce is TRUE. (2020-08-28, Fri)

                    Changes in version 1.1.9                        
  

• update ggordpoint to fit the usage when user want to set mapping by manually. (2020-08-25, Tue)

                    Changes in version 1.1.8                        
  

• get_taxadf, get_alltaxadf and diff_analysis has supported function datasets or other type datasets. (2020-08-17, Mon)

                    Changes in version 1.1.7                        
  

• bugfix: cladetext argument has been omitted in ggdiffclade, now it has been fixed. (2020-08-14, Fri)

• deprecated argument: the size argument controlled the width of line of tree has been deprecated. The linewd replace it (2020-08-14, Fri).

                    Changes in version 1.1.6                        
  

• removeUnkown argument has been replaced with removeUnknown in ggdiffbox, ggeffectsize, ggdifftaxbar and ggdiffclade. (2020-08-12, Wed)
• class argument has been replaced with classgroup in diff_analysis. (2020-08-12, Wed)

• add inward_circular layout in ggdiffclade. (2020-08-12, Wed)

                    Changes in version 1.1.5                        
  

• ggdifftaxbar supports png, tiff format. (2020-08-10, Mon)

• add stop information to state the class argument in diff_analysis. (2020-08-10, Mon)

                    Changes in version 1.1.4                        
  

• add tax_table information to result of get_taxadf. (2020-08-07, Fri)

                    Changes in version 1.1.3                        
  

• change according to dplyr (v=1.0.0) (2020-08-05, Wed)
• remove rename_ and group_by_

• modified the angle to 90 in ggdiffclade when layout is slanted or rectangular (2020-08-05, Wed)

                    Changes in version 1.1.2                        
  

• fix a bug. When the first rank taxa level (Kingdom) is NA.

miRSM

                 Changes in version 1.7.2-1.7.3                     

• Update miRSM.R <2020-09-18, Fri>

                    Changes in version 1.7.1                        
  

• Update module_Coexpress function <2020-08-21, Fri>

mitch

                   Changes in version 1.0.12                        

• A fix to problems in >3D plots caused by contrast names

mixOmics

                   Changes in version 6.14.0                        

new features / enhancements / changes

• circosPlot: The radial location of feature names can now be cutomised using var.adj
• added plot and print methods for nipals ouput (#87)
• all Discriminat Analyses now run solely on mode=regression (#79)
• cim argument change: threshold replaced by cutoff
• nipals and pca with missing values allow skipping reconstitution of the input matrix
• tune.block.splsda now allows random number seed also for parallel processing (#72)
• New biplot methods for the pca family (#90)

bug fixes

• plotIndiv: Legend bug which misspecified the groups resolved
• plotIndiv: Legends now ordered as inputted, and not alphabetically
• plot method issue for spca resolved
• plotLoadings.spca bug with var.names now fixed (#81)
• ipca deprecation warning fixed

MOFA2

                   Changes in version 0.99.0                        

• submitted package to Bioconductor

MOGAMUN

                   Changes in version 0.99.0                        

• Submitted to Bioconductor.

motifStack

                   Changes in version 1.33.14                       

• remove reverse complement alignment for RNA motifs.

                   Changes in version 1.33.13                       
  

• narrow the predefined font.

                   Changes in version 1.33.12                       
  

• fix the issue for pcm2pfm if the column counts are not identical.

                   Changes in version 1.33.11                       
  

• update the markers to allow label + line/rect.

                   Changes in version 1.33.10                       
  

• add alignment function for AA motifs.

                   Changes in version 1.33.9                        
  

• fix the issue for AA motif of clusterMotifs

                   Changes in version 1.33.8                        
  

• fix the issue of symbol position for predefined font

                   Changes in version 1.33.7                        
  

• update check ghostscript

                   Changes in version 1.33.6                        
  

• fix the bug in pcm2pssm

                   Changes in version 1.33.5                        
  

• fix the bug in pcm2pssm

                   Changes in version 1.33.4                        
  

• add pssm class

                   Changes in version 1.33.3                        
  

• replace MotIV by matalign.

• add cutoffPval for motifSignature function.

                   Changes in version 1.33.2                        
  

• add parameter environment for coloredSymbols

                   Changes in version 1.33.1                        
  

• change grImport, grImport2 and MotIV to Suggests.

• use roxygen2 to generate help files.

MouseFM

             Changes in version 0.99.9 (2020-08-23)                 

• Check package bugfix in getURL function

             Changes in version 0.99.8 (2020-08-13)                 
  

• Getter/Setter for URL of backend server

             Changes in version 0.99.7 (2020-06-08)                 
  

• Updated database

• New authors

             Changes in version 0.99.1 (2020-05-22)                 
  

• Updated .gitignore

             Changes in version 0.99.0 (2020-05-21)                 
  

• Submission to Bioconductor

             Changes in version 0.1.0 (2020-05-04)                  
  

• Creation

msa

                   Changes in version 1.21.1                        

• changed msaClustalW() examples to run smoothly on Windows with R 4.0.x

• added warning to msaClustalW() help page regarding cluster=”upgma” on Windows

                   Changes in version 1.21.0                        
  

• new branch for Bioconductor 3.12 devel

MsCoreUtils

                     Changes in version 1.1                         

Changes in 1.1.7

• Rewrite c(“left”, “right”, “inner”, “outer”) join in C <2020-10-06 Tue>.

Changes in 1.1.6

• Rewrite closest in C <2020-09-24 Thu>.
• Fix #65 and #66.

Changes in 1.1.5

• Add … to functions to join and compare peaks; see also #131.

Changes in 1.1.4

• Change references to Feature to QFeatures <2020-07-14 Tue>
• Ensure closest accept just argument tolerance of length 1 or length(x); see also #61, PR #62 <2020-08-07 Thu>.
• The tolerance argument in closest should now be of length 1 or of length(x) (was length(table) before) <2020-08-20 Thu>.

Changes in 1.1.3

• For an empty table closest and common return a vector of length x with NA or FALSE, respectively (instead of 1 and TRUE). Fixes #55 <2020-06-18 Thu>.
• closest and common ignore NA in table <2020-06-19 Fri>.
• Fix rbindFill for single data.frame or DataFrame as input <2020-06-23 Tue>.

Changes in 1.1.2

• New colCounts() aggregation function <2020-05-27 Wed>.

Changes in 1.1.1

• Add some popular distance/similarity metrices: ndotproduct neuclidean navdist nspectraangle; see also PR #33.

• Add deprecation note to dotproduct <2020-05-22 Fri>.

Changes in 1.1.0

• Bioconductor devel version (Bioc 3.12)

MSEADbi

                   Changes in version 0.99.0                        

• Package released

msImpute

                   Changes in version 0.99.26                       

• update doc for msImpute

                   Changes in version 0.99.25                       
  

• fix typo in msImpute man page

                   Changes in version 0.99.24                       
  

• Bug fix in the internal function l2bary

                   Changes in version 0.99.23                       
  

• selectFeatures and msImpute now use information theoretic approaches to find informative features for MAR/MNAR diagnosis and estimation of optimal rank, respectively.

• lambda in msImpute is now estimated from the data, using the bayesian interpretation of this shrinkage operator.

• msImpute can be run in three modes: “v1” is the original implementation of softImpute-als algorithm, “v2” is the enhanced low-rank estimation implemented in this version update, “v2-mnar” is adaptation of low-rank models for MNAR data. More details about methods in documentation.

                   Changes in version 0.99.22                       
  

• Submitted to Bioconductor

MSnbase

                    Changes in version 2.15                         

Changes in 2.15.7

• Fixed some consistency in the processing reporting (contributed by @stanstrup).

Changes in 2.15.6

• Add extractSpectraData function to extract all data from an MSnExp or Spectra object as a DataFrame to be used with the Spectra package.

Changes in 2.15.5

• combineSpectraMovingWindow gains parameter ppm to allow definition of m/z relative differences.

Changes in 2.15.4

• Add splitByFile,OnDiskMSnExp method to provide a more efficient splitting.

Changes in 2.15.3

• Rename Spectra class to MSpectra.
• Rename Chromatograms class to MChromatograms.

Changes in 2.15.2

• Add MSnbase2 citation entry <2020-05-15 Fri>

Changes in 2.15.1

• Fix: don’t read mzTab twice <2020-05-05 Tue>

Changes in 2.15.0

• Bioconductor devel version (Bioc 3.12)

MSPrep

             Changes in version 0.99.0 (2020-10-02)                 

• Submitted to Bioconductor

msPurity

                   Changes in version 1.15.1                        

• Update dev to match bug fixes in master

                   Changes in version 1.14.1                        
  

• Update of rdpc algorithm (see https://github.com/computational-metabolomics/msPurity/issues/78)

• Update of align algorithm (see https://github.com/computational-metabolomics/msPurity/issues/79)

• Fix for spectralMatching of type ‘scan’ previously incorrectly outputing no matches

MSstatsConvert

                   Changes in version 0.99.0                        

• Added logging utitilies: MSstatsLogsSettings, MSstatsSaveSesionInfo.
• Added functions for importing and cleaning data: MSstatsImport, MSstatsClean.
• Added functions for preprocessing: MSstatsMakeAnnotation, MSstatsPreprocess, MSstatsBalancedDesign.

• Added vignette.

                    Changes in version 0.0.1                        
  

• Added a NEWS.md file to track changes to the package.

MSstatsPTM

             Changes in version 0.99.0 (2020-09-28)                 

• Submitted to Bioconductor

MSstatsTMT

             Changes in version 1.6.6 (2020-10-13)                  

• Fix the bug in converters due to fractions with same mean, sum and max values

• Fix the bug in converters due to summaryforMultipleRows

• Fix the bug in OpemMS converter due to duplicated rows

             Changes in version 1.6.3 (2020-06-05)                  
  

• Allow NA in the annotation file

             Changes in version 1.6.2 (2020-06-02)                  
  

• Fix the bug in proteinSummarization() function and make sure the input to dataProcess is data.frame

             Changes in version 1.6.1 (2020-05-10)                  
  

• Update groupComparisonTMT() to make predictions for every protein

MSstatsTMTPTM

             Changes in version 0.99.0 (2018-09-21)                 

• Submitted to Bioconductor

MultiAssayExperiment

                   Changes in version 1.16.0                        

New features

• Coercion methods from list/List to MultiAssayExperiment method now available.

Bug fixes and minor improvements

• Provide more details in documentation for mergeReplicates
• Improved documentation for accessor function return values, helper function examples (@llrs, #281)
• Fixed bug when using longFormat with character assay matrices (@jonocarroll, #282)

multicrispr

             Changes in version 0.99.0 (2020-04-24)                 

• Submitted to Bioconductor

multiGSEA

                   Changes in version 0.99.0                        

• Package added to Bioconductor

multiHiCcompare

             Changes in version 1.7.1 (2020-08-28)                  

• Track NEWS

• Bump version

• Update R version dependency from 3.5.0 to 4.0

• Add exported objects to NAMESPACE that caused BiocCheck error

• Add CITATION, also to README.md file

• Update DESCRIPTION o Add Mikhail Dozmorov as Maintainer o Add URL and BugReports fields

musicatk

            Changes in version 0.99.10 (2020-10-02)                 

PRE-RELEASE

• Pre-release version of the musicatk package to be submitted to Bioconductor

NanoMethViz

                    Changes in version 1.0.0                        

• Initial Bioconductor release

NBAMSeq

             Changes in version 1.5.1 (2020-05-04)                  

• Updated citation

ncRNAtools

             Changes in version 0.99.9 (2020-10-01)                 

• Reverted changes introduced in 0.99.6

• Set SSL security level to 1 in Linux environment to bypass a bug in OpenSSL 1.1.1

             Changes in version 0.99.6 (2020-09-29)                 
  

• Changed all URLs to http to prevent issues when accessing websites via HTTPS due to a bug in OpenSSL 1.1.1

             Changes in version 0.99.4 (2020-09-07)                 
  

• Introduced changes suggested during Bioconductor review

             Changes in version 0.99.0 (2020-07-24)                 
  

• Submitted to Bioconductor

Nebulosa

                   Changes in version 0.99.94                       

• Color scale based now on scale_color_viridis_c()

                   Changes in version 0.99.93                       
  

• Stable version for bioconductor release

                   Changes in version 0.99.92                       
  

• Sets up BiocCheck requirements

netDx

                    Changes in version 1.1.4                        

Changes

• New functionality to smooth mutations over interaction, starting from sparse

somatic mutations

• BiocFileCache usage update

NewWave

             Changes in version 0.99.5 (2020-09-08)                 

• Modification to optimd function to prevent decreasing of the likelihood function when appling mini-batch with commonwise dispersion

             Changes in version 0.99.0 (2020-09-08)                 
  

• Submit to bioconductor

             Changes in version 0.2.0 (2020-09-07)                  
  

• Matrix and Delayed array framework complete running

ngsReports

                    Changes in version 1.5.5                        

• Added importSJ for importing SJ.out.tab files from the aligner STAR

• Added plotType = “residuals” for plotSeqContent()

                    Changes in version 1.5.4                        
  

• Allowed for ignoring basename() calls in all importNgsLogs functions

• Added cumulative GC plot to plotGcContent() as plotType = “cdf”

• Changed plotting option name from cumulative to cdf for plotSeqLengthDistn()

• Announced deprecation of runFastQC()

                    Changes in version 1.5.3                        
  

• Fixed bug in plotOverrep

Omixer

                    Changes in version 0.99                         

• Initial release to Bioconductor.

• Added NEWS file.

• Changed image paths in vignette.

OmnipathR

             Changes in version 1.99.0 (2020-10-03)                 

• New tests
• Many little bugfixes
• Updated package metadata

• Preparation for Bioconductor 3.12

             Changes in version 1.3.4 (2020-08-04)                  
  

• License and password handling

• Can be directed to different server by options

             Changes in version 1.3.1 (2020-06-05)                  
  

• Addition of the package website.
• Modification of the pdf vignette for an html one.
• Major refactoring of functions.
• Addition of the intercellular network function.
• Modification for the intercellular categories.

OncoSimulR

             Changes in version 2.19.2 (2020-06-03)                 

• Updated ctb: added Magellan and exprTk and clarified contributions.

             Changes in version 2.19.1 (2020-05-05)                 
  

• Occasional failures of @test.sample-prob.R#42 in Windows 386

             Changes in version 2.19.0 (2020-05-05)                 
  

• Bumped version to match current Biocdevel.

onlineFDR

                    Changes in version 1.8.0                        

MODIFICATIONS

• harmonised inputs to algorithms

• added unit tests

• updated authors

openCyto

                    Changes in version 3.11                         

Enhancements

• Allow control of mininum number of events for each step of GatingTemplate #298

Bug Fixes

• Handle a few more edge cases in .improvedMinDensity

• Added a fix to the density estimate used by gate_tautstring

                    Changes in version 3.10                         
  

API Changes

Simple renaming

• gate_flowClust_1d -> gate_flowclust_1d
• gate_flowClust_2d -> gate_flowclust_2d
• tautStringGate -> gate_tautstring
• templateGen -> gh_generate_template
• add_pop_init -> gs_add_gating_method_init
• add_pop -> gs_add_gating_method
• remove_pop -> gs_remove_gating_method
• get.helperGates -> gs_get_helpergates
• toggle.helperGates -> gt_toggle_helpergates
• delete.helperGates -> gs_delete_helpergates
• getNodes -> gt_get_nodes
• getParent -> gt_get_parent
• getChildren -> gt_get_children
• getGate -> gt_get_gate
• gating -> gt_gating

• registerPlugins -> register_plugins

  Classes and methods no longer exported

• registerGatingFunction
• gtMethod
• gtPopulation
• polyFunctions
• ppMethod

Bug Fixes

• Some minor fixes to gt_toggle_helpergates
• Fix “positive” argument to gate_mindensity to match doc

OrganismDbi

                   Changes in version 1.32.0                        

BUG FIXES

• (v. 1.31.1) Load OrganismDb objects even if not on search path. See https://support.bioconductor.org/p/134141/

OUTRIDER

                    Changes in version 1.7.1                        

• Move to S3/S4 methods to be compatible with FRASER

• Due to the S3/S4 changes minor changes in the argument names happend mainly ods -> object or x

• Bugfixes: #29

padma

              Changes in version 0.99                   

• Substantial changes to prepare for Bioconductor submission o added S4 classes / methods / generics o integration with MultiAssayExperiment

              Changes in version 0.1 (2020-01-09)                   
  

• Initial development version

pageRank

             Changes in version 0.99.0 (2020-09-21)                 

• Submitted to Bioconductor

PAST

             Changes in version 1.4.1 (2020-04-30)                  

• bug fixes and new minimum R version

pathview

                   Changes in version 1.29.1                        

• developmental version now available on GitHub at: https://github.com/datapplab/pathview

• fixed warning on “requireNamespace(pkg.name)” in geneannot.map.R and sim.mol.data.R. Now “import” from org.Hs.eg.db, instead of “suggest” it. Also import more functions and class from AnnotationDbi.

• prevented potential error caused by class(exprs) == “data.frame” or “class()==” if conditions in multiple functions. class(exprs) now returns a vector of length 2, which caused the error.

pcaExplorer

                   Changes in version 2.16.0                        

Other notes

• Replaced dependency from d3heatmap with the functionality of heatmaply

PCAtools

                    Changes in version 2.2.0                        

• added support to overlay variable loadings arrows on biplot

• better positioning of PC labels in triangular pairs plot

• added functionality to encircle groups of samples

• added functionality to draw stat ellipses with confidence intervals

• users can now add legend titles and these will be added by default

peakPantheR

             Changes in version 1.3.4 (2020-10-23)                  

• Add missing function export for GUI

             Changes in version 1.3.3 (2020-10-11)                  
  

• Shiny Graphical User Interface

             Changes in version 1.3.2 (2020-09-29)                  
  

• Unittest numerical precision correction for Ubuntu 20.04.1 LTS

             Changes in version 1.3.1 (2020-09-21)                  
  

• Retention time correction procedure based on reference compounds

• Exponentially Modified Gaussian (EMG) peak fitting

PepsNMR

             Changes in version 1.7.1 (2020-07-21)                  

BUG CORRECTION

• Debugged ReadFid when the type of raw data is double (i.e. if DTYPA==2)

periodicDNA

                    Changes in version 0.3.2                        

• IMPORTANT:

• Implemented data-raw for reproducibility

• MINOR:

• Changed xlim of norm. distr. plot in plotPeriodicityResults()

             Changes in version 0.3.1 (2020-05-05)                  
  

• IMPORTANT:

• rollmean(k=3) is now applied before normalisation as well, on the raw distribution vector
• plotPeriodicityResults() output returns one single plot (with cowplot)
• getPeriodicityTrack() now returns the Rle
• Improved plotting functions -now show shuffled for plotPeriodicityResults()

• Added ggplot2 theming

• MINOR:

• Changed many variable names (all to snake_case)
• sampleGRanges is now full-fledged function (GRanges, DNAStringSet, character and BSgenome methods)
• sampleGenome is an alias for sampleGRanges.character
• Added sacCer3 to getPeriodicity BSgenomes
• Added DNAString method for getPeriodicity
• Added a vignette describing the internal steps
• Clarified user-level functions in README
• Added ce11_TSSs data
• Renamed generateperiodicitytrack as getPeriodicityTrack
• Renamed variables in getFPI and getPeriodicity

• Created a utility char2BSgenome()

             Changes in version 0.3.0 (2020-05-03)                  
  

• Added tests
• Added getFPI function
• cleaned-up functions
• cleaned-up function dependencies
• Added toy data

• Added vignette

             Changes in version 0.2.1 (2020-03-04)                  
  

• Added Travis build check
• Simplified README.md

PGA

                   Changes in version 1.19.1                        

• set2key, set2keyv, and key2 of data.table were deprecated and had been removed.

phantasus

                    Changes in version 1.9.5                        

• Support for preloaded sessions

                    Changes in version 1.9.3                        
  

• Changed Dockerfile to nginx+rApache (default ports are changed)

PharmacoGx

                   Changes in version 2.1.12                        

• Added experimental support for a new class, the LongTable, for storing the sensitivity data in a PharmacoSet.
• Because this is not well tested, we have left not updated the PSets available via the downloadPSets function.
• Instead we have provided a convenient function, convertSensitivitySlotToLongTable, which takes in a PharmacoSet object, converts the data in the @sensitivty slot to a LongTable and returns an updated PharmacoSet object.
• The LongTable class will be used in the future to allow PharmacoSets to store treatment response experiments with multiple drugs or cell-lines, greatly expanding the variety of data which can be stored in a PharmacoSet object.
• For more details on the LongTable class, please see the vignette in the CoreGx package.

PhosR

                    Changes in version 0.1.5                        

• Significant updates and addition to the documentation
• Major changes to code writing style to comply with BioC
• Updated TC example data

PhyloProfile

                   Changes in version 1.3.11                        

• Add filter number of co-orthologs to parseInfoProfile()

                   Changes in version 1.3.10                        
  

• Calculate percentage of present taxa after filtering of var1 and var2

• Fixed filter when working with high taxonomy ranks

                    Changes in version 1.2.8                        
  

• Added new NCBI taxonomy ranks (e.g. biotype, isolate, pathogroup, …)

• Added function to reset taxonomy data

                    Changes in version 1.2.7                        
  

• Solved problem with new NCBI taxonomy rank “clade” by replace them with “norank”

                    Changes in version 1.2.6                        
  

• Fixed bug customized profile of subset of taxa not clickable

                    Changes in version 1.2.4                        
  

• Fixed bug checking invalid taxon IDs

                    Changes in version 1.2.1                        
  

• Fixed bug in rankIndexing and processNcbiTaxonomy

• Improved check for invalid input taxon IDs

Pigengene

            Changes in version 1.15.20 (2020-09-28)                 

Changes in existing functions

• When automatically computing the threshold in the consensus function, we now do not allow it to be more than 1 to be compatible with bnlearn 4.6.1.

            Changes in version 1.15.16 (2020-09-22)                 
  

Changes in existing functions

• The modules can now be determined in the module.heatmap function using the new mes argument.

            Changes in version 1.15.14 (2020-09-08)                 
  

Bug Fixes

• combine.networks now really removes the big TOM file when doRemoveTOM=TRUE.

            Changes in version 1.15.12 (2020-06-22)                 
  

Changes in existing functions

• The DiseaseColors argument in the plot.pigengene function can now be set automatically.

Bug Fixes

• pheatmap.type now works fine even when the number of samples in a condition is only 1.

pipeComp

            Changes in version 0.99.43 (2020-07-20)                 

• there is now the possibility to continue runs despite errors, and enlarged merging capacities

            Changes in version 0.99.27 (2020-04-29)                 
  

• the plotting functions for the scRNAseq clustering pipeline (scrna_evalPlot_DR and scrna_evalPlot_clust) have been replaced by more flexible, pipeline-generic functions (evalHeatmap) and a silhouette-specific plotting function (scrna_evalPlot_silh). The general heatmap coloring scheme has also been changed to make meaningful changes clearer.

            Changes in version 0.99.23 (2020-04-21)                 
  

• Added SVA-DEA pipeline and vignette

• Standardized results heatmaps for any PipelineDefinition

             Changes in version 0.99.7 (2020-04-01)                 
  

• Submitted to Bioconductor

             Changes in version 0.99.3 (2020-02-07)                 
  

• made important changes to the scRNAseq pipeline, greatly simplifying the format of the output. As a consequence, results produced with older version of the package are not anymore compatible with the current version’s aggregation and plotting functions.

plyranges

                    Changes in version 1.9.3                        

• minor spelling and layout fixes to vignette,

• @PeteHaitch corrected table layout in vignette

                    Changes in version 1.9.2                        
  

• minor documentation fixes

                    Changes in version 1.9.1                        
  

• Spencer Nystrom has made several significant contributions to the join_nearest family of functions:

1. join_nearest_(x, y, …, distance = TRUE) family of functions now takes a new argument, distance, which allows the user to add a column for the distance of the nearest range y to that in x.
2. add_nearest_distance_(x, y, …) family of functions, which will add a new metadata column to the x ranges object which contains the distance to its nearest neighbor in y. If there are no nearest neighbors, the new column will be given a missing value.

polyester

                   Changes in version 1.99.3                        

• NB function now exported

• note that version 1.99.3 on GitHub was version 1.1.0 on Bioconductor.

                   Changes in version 1.99.2                        
  

• bug fix in fragment generation (last 2 bases of transcript were never sequenced)

POMA

                   Changes in version 0.99.45                       

• PomaOutliers bug fixed
• New references in PomaRankProd help
• PomaLimma and PomaUnivariate bug related with one covariate analysis fixed

• The elbow method to calculate the optimum number of clusters has been added in PomaClust function

                   Changes in version 0.99.37                       
  

• POMA has been accepted to Bioconductor!
• PomaRankProd minor bug fixed
• Authors updated

• Bioconductor logo

                   Changes in version 0.99.33                       
  

• All Bioconductor issues in the review process have been addressed

• POMA EDA vignette added

                   Changes in version 0.99.16                       
  

• BiocCeck requirements fixed
• Examples added in functions

• pkgdown files removed from master branch

                   Changes in version 0.99.0                        
  

• POMA is now submitted to Bioconductor!
• All features implemented work as expected
• All tests finished
• Achieved desired coverage (>95%)
• Vignettes and documentation are ready for the first release

preciseTAD

             Changes in version 0.99.6 (2020-08-30)                 

• Major simplification of the preciseTAD function, many arguments are kept default

• Major vignette rewrite

• Add pkgdown web site

• Update DESCRIPTION o Package description

• Start tracking NEWS

             Changes in version 0.99.4 (2020-07-14)                 
  

• Preparing for release

             Changes in version 0.99.0 (2020-06-16)                 
  

• Initial version

proActiv

                   Changes in version 0.99.0                        

• Submitted to Bioconductor

proDA

                     Changes in version 1.3                         

• Escape result coefficient names if result_names() is called and they contain potentially problematic characters (see issue #4)

progeny

           Changes in version 2020-10-14 (2020-10-14)               

• Model matrices are not accessed in the local and not in the global enviroment

           Changes in version 2020-09-01 (2020-09-01)               
  

• Fixed issue with rownames when using Progeny with Permutations function

           Changes in version 2020-06-09 (2020-06-09)               
  

• Website: Google Analytics

           Changes in version 2020-04-27 (2020-04-27)               
  

• PROGENy website development

Major update with the following main points:

• Added the mouse model matrix containing 14 pathways

• The human model matrix extended to 14 pathways

• Added the following functions: progenyPerm, progenyScatter, progenySavePlots, getModel

• Added tests and test data

• Added the vignette for usage the PROGENy on single-cell RNA-seq data

• Added functionality to work with Seurat objects

pRolocGUI

                    Changes in version 1.99                         

CHANGES IN VERSION 1.99.2

• fixed warning in profiles plot
• fixed colour matching in factet plot

CHANGES IN VERSION 1.99.1

• Apps updated to new shinydashboardPlus style
• Options to save plots as high res images
• User set colourpicker for creating figures
• Support for data export to csv
• Support batch import searching
• PCA app has been replaced with explore app
• New aggregation app
• Classify app removed

psichomics

                   Changes in version 1.14.4                        

• Improve file browser dialog:
• Now correctly allows to select a single file in macOS
• Now correctly allows to select a directory in Windows
• Correctly set default location when opening a file in Linux
• Internal improvements
• Data loading:
• Improve performance when loading compressed data (GZ and BZ2 files)
• Increase optional verbosity while loading files
• Speed up loading of VAST-TOOLS’ inclusion levels
• Fix loading of VAST-TOOLS’ inclusion levels sometimes returning an error regarding duplicated row names
• Fix issues with missing values as alternative splicing event complexity in VAST-TOOLS’ inclusion levels

• Copy-edit tutorials on loading user-provided data and using the command-line version

                   Changes in version 1.14.3                        
  

• Fix unit tests due to changes in Ensembl API response

                   Changes in version 1.14.2                        
  

Support for loading more data formats

• getSplicingEventData(): get a table with all information for a given dataset of alternative splicing quantification data
• VAST-TOOLS inclusion levels and gene expression tables:
• Import VAST-TOOLS’ output files (inclusion levels, cRPKMs and gene read count tables); in the visual interface, use the User-provided data loading panel and load a specific alternative splicing quantification or load the folder containing such file; in the command-line interface, use loadLocalFiles()
• To parse splicing event from VAST-TOOLS in the command-line interface, use for instance parseSplicingEvent(“HsaEX0007927”, data=VASTTOOLSpsi)
• Support for importing inclusion tables with arbitrary alternative splicing event identifiers (information for these events will not be available, such as event type and cognate gene)
• SRA metadata:
• Automatically load metadata from the SRA Run Selector (usually comes in files named SraRunTable.txt) avoiding the need to use prepareSRAmetadata() first
• GTEx data loading (loadGtexData()):
• Support for loading GTEx data from V8, V7, V6 or V4 releases
• Organise GTEx data into folders named based on release version
• Copy-edit tutorial on loading user-provided data

New features

• plotSplicingEvent():
• Alternative splicing diagrams now render automatically instead of showing SVG code (if printing more than one event, a table is displayed with event identifiers and respective diagrams)
• Plot intron retention events (e.g. from VAST-TOOLS)
• plotLibrarySize(): plot library size from gene expression data
• Alternative splicing quantification filtering (visual interface):
• New panel to allow filtering already loaded alternative splicing quantification based on event types, samples, PSI statistics (such as median, variance and range) and cognate genes (some filtering steps may not be available when using user-provided tables with inclusion levels)
• Filter data based on individual PSI values (also available when quantifying alternative splicing)
• Filter VAST-TOOLS events based on its quality scores for read coverage
• Toggle specific statistics based on alternative splicing quantification values when filtering
• Preview the original and filtered events in an easy-to-use plot
• Gene expression filtering:
• Toggle specific statistics based on gene expression values when filtering (visual interface)
• Arguments used in filterGeneExpr() and normaliseGeneExpression() are now returned as attributes of those functions
• Differential analysis:
• Tooltips of volcano plots now include diagram of alternative splicing events
• Gene, transcript and protein annotation (visual interface):
• Suggest genes based on loaded data
• Change species and assembly when fetching information
• Improve interface of PubMed article query, including persistent user-inputted tags even when changing selected gene
• Improve relevance of results from PubMed articles
• Much faster calculation of row/column-wise means, medians, variances and ranges (helpful for plotting statistics of large datasets)
• Include Dockerfile to create Docker images based on code revisions

Bug fixes and minor changes

• Progress bar is now animated as in previous versions
• Data loading (visual interface):
• Allow to discard selected files in file browser input elements
• When creating groups by sample index/identifiers, suggest sample names not only obtained from sample information, but also from alternative splicing quantification and gene expression datasets
• “Browse…” button now opens file browser to select folder where data is stored (as expected) in GTEx and SRA panels
• Only pre-create groups of genes (based on literature-based gene lists) if at least one of its genes exists in any of the loaded datasets
• Correctly parse gene symbols containing underscores
• Fix gene expression summary plots not showing in specific situations
• Fix library size plot not working properly and causing rendering issues
• Fix settings used to quantify alternative splicing not showing up
• Show errors raised while reading a file (e.g. if file is too big for available memory)
• Show alert if no GTEx data options are selected
• Show filename of the file used to load gene expression and alternative splicing data from GTEx and SRA
• Show helpful context messages in panel interfaces
• Improve visual interface and minor copy-editing
• Local data loading:
• Support loading data from GTEx V8 or previous releases
• Fix bad formatting of help tooltips when using shiny 1.4.0 or newer (visual interface)
• Gene expression filtering:
• Hide message regarding the usage of no design matrix
• Alternative splicing annotation:
• Try to load cached alternative splicing annotation if a timeout occurs
• Include gene symbols in custom annotations if available
• Account for possible filename changes when parsing annotations from VAST-TOOLS, rMATS, SUPPA and MISO
• Alternative splicing event selection (visual interface):
• Include loading indicator while searching for events
• Decrease number of operations performed after selecting an event
• Fix crash when changing to an alternative splicing quantification dataset without the selected splicing event
• Allow to search using an event identifier directly
• Show event identifier instead of prettier identifier to avoid confusion
• Data grouping (visual interface):
• Simplify group selection interface
• Fix suggested attributes and index/identifiers in group creation not being cleared when changing to datasets where such data is unavailable (thus showing the attributes/index/identifiers of the previous dataset)
• Show an alert when there is no data to create groups
• Dimensionality reduction:
• performPCA() and performICA() now directly raise errors (instead of simply capturing and returning them)
• PCA: loading plots now show parsed information of events (cognate gene, event type and genomic position) if available
• PCA: the correct splicing event is now selected when clicking on any loadings in the loadings plot (visual interface)
• Differential analyses (visual interface):
• Use group colours in density plots of differential expression table
• Fix occasional crash when performing differential analyses with different number of groups during the same session
• Tooltips of volcano plots are now properly positioned in high-resolution screens
• The correct splicing event is now selected when clicking the density plots or survival curves in the table
• When creating a group from differential splicing results, correctly set cognate genes of alternative splicing events
• diffAnalyses(): deprecated psi argument was now removed
• Distribution plots (plotDistribution()):
• After hiding all plot series, hide Y axis (rug plots of the different groups have arbitrary Y values to easily distinguish them)
• Rug plots of gene expression density plots are now placed near the X axis as expected
• Correlation analyses (visual interface):
• Warn when selecting genes that are not available in the selected gene expression dataset (instead of crashing the app)
• print() extended to better display information on gene list objects; e.g. print(getGeneList())
• Fix issues when installing the package:
• Fix error when unit testing in R 4.0 or higher (strings in data frames are not converted to factors by default)
• Fix R CMD check warning of Unicode symbol translation in Windows

• Fix comparing signed and unsigned integers in Rcpp functions

                   Changes in version 1.14.1                        
  

Fix unit tests for R 4.0

PureCN

                   Changes in version 1.20.0                        

NEW FEATURES

• Support for GATK4 GenomicsDB import for mapping bias calculation

• Added –additionaltumors to PureCN.R to provide coverage files from additional biopsies from the same patient when available

• PSCBS segmentation now identifies on-target breakpoints first when off-target is noisy, thus boosting sensitivity in on-target regions

• Beta-binomial model in runAbsoluteCN now uses the fits in mapping bias database. We plan to set this as default in upcoming versions and appreciate feedback.

SIGNIFICANT USER-VISIBLE CHANGES

• We now check if POP_AF or POPAF is -log10 scaled as new Mutect2 versions do.

• Added support for GERMQ info field containing Phred-scaled germline probabilities.

• Detect Mutect2 VCF more reliably

• Updated Mutect2 failure flags: “strand_bias”, “slippage”, “weak_evidence”, “orientation”, “haplotype”

• Removed defunct normal.panel.vcf.file from setMappingBiasVcf

• Removed defunct interval.weight.file from segmentationPSCBS, segmentationCBS and processMultipleSamples

• Made calculateIntervalWeights defunct

• Changed default of min.normals in calculateMappingBiasVcf/Gatk4 to 1 from 2

• Changed default of –signature_databases to “signatures.exome.cosmic.v3.may2019” (v3 instead of v2)

• Now warn if recommended -funsegmentation is not used

• Added parallel option for callAmplificationsInLowPurity

• callMutationBurden now uses all non-filtered targets as callable region when callable is not provided

• plotAbs in chromosome mode now displays wider range of log2 ratios (makes it possible to examine outliers)

• Moved vcf.field.prefix from predictSomatic to runAbsoluteCN since it now adds more fields like prior somatic and mapping bias to the VCF

• Changed default of runAbsoluteCN min.ploidy to 1.4

BUGFIXES

• Fix for crash with CNVkit input when log-ratio contained highly negative outliers

• Fixed a bug in preprocessIntervals/IntervalFile.R when input contained overlapping and stranded intervals

• Fix for crash when GC-correction is attempted on empty coverage (for example off-target region without any off-target reads)

• Fix for crash when VCF FA field contained missing values

• Fix for a bug in callAmplificationsInLowPurity that can cause a wrong chromosome percentile

QFeatures

                    Changes in version 0.99                         

QFeatures 0.99.4

• Fix: improved nNA with new implementation and additional unit tests <2020-10-23 Fri>

QFeatures 0.99.3

• New feature: the longFormat function returns a long DataFrame with quantitative data along with metadata (see #116) <2020-10-8 Thu>
• New feature: the rowData method returns a list containing the rowData for all assays (see #86) <2020-09-16 Wed>
• Keep colnames when reading a single column assay (see #108) <2020-09-09 Wed>

QFeatures 0.99.2

• Added infIsNA.
• Add Christophe Vanderaa as an author.

QFeatures 0.99.1

• Address comments Bioconductor review (see submission issue for details.

QFeatures 0.99.0

• Bioconductor submission

qPLEXanalyzer

                    Changes in version 1.7.3                        

• Fix limits of scale in corrPlot to c(0, 1)

• Fix bug in regress intensities where control columns were not being removed

                    Changes in version 1.7.1                        
  

• Change Vignette to HTML

• Add textsize argument to corrPlot

• Allow missing values in scaling normalisations

QuasR

                   Changes in version 1.30.0                        

NEW FEATURES

• added binSize argument for qProfile

RadioGx

                    Changes in version 1.0.1                        

• Abstract further functionality from RadioGx into CoreGx dependency package

• Harmonize function and API design to be in line with PharmacoGx R package

                    Changes in version 1.0.0                        
  

• RadioGx archived on CRAN for submission to Bioconductor
• Molecular profile data has been migrated from ExpressionSet to SummarizedExperiment to allow incorporation of multiple assays as well as to be in line with Bioconductor best practices
• Wrote a vignette to highlight simple usage of the package

RaggedExperiment

                   Changes in version 1.14.0                        

Bug fixes and minor improvements

• Update package to changes in MatrixGenerics (new location of the rowRanges generic)

randRotation

             Changes in version 1.1.1 (2020-09-23)                  

• Function contrastModel() added to support contrast rotation

• Vignette extended

• Deprecate function df_estimate()

rBiopaxParser

                   Changes in version 2.29.1                        

• Removed functionality for transitive reduction, which was imported from nem package (dropped out of Bioconductor).

RCy3

                   Changes in version 2.10.0                        

• New functions:
  • getCurrentStyle, #15
• Added Sys.sleep to buggy CyREST steps in…
  • createNetworkFromDataFrames, #98
  • importNetworkFromFile
  • importNetworkFromNDEx
  • exportNetworkToNDEx
  • updateNetworkInNDEx
  • importFilters
  • create***Filter
  • applyFilter
  • updateStyleMapping
  • setVisualPropertyDefault

• Refactored getNetworkViewSuid

• Handled special 404 cases in .cyError

• Bug fix #94: added base.url param

• Overhauled error handling and messaging

ReactomeGSA

             Changes in version 1.3.6 (2020-09-01)                  

• Improved analyse_sc_clusters for SingleCellExperiment objects to define cell grouping using factors and a single character string specifying the metada field.

             Changes in version 1.3.4 (2020-09-01)                  
  

• Fixed bug in analyse_sc_clusters when processing SingleCellExperiment objects.

             Changes in version 1.3.3 (2020-05-26)                  
  

• Updated documentation

             Changes in version 1.3.2 (2020-05-26)                  
  

• Added workaround for SEC_E_ILLEGAL_MESSAGE error on older Windows systems.

             Changes in version 1.3.1 (2020-04-29)                  
  

• Added option to hide non-significant pathway in plot_correlations

reconsi

                    Changes in version 1.1.2                        

• Revert to nonparametric null estimation

• Random tiebreaking is by default off for reconsi(), but on for testDAA()

                    Changes in version 1.1.1                        
  

• Renamed “permZvals” argument to “resamZvals”, which is more accurate
• Allow pi0 to be provided rather than estimated
• Actualized return arguments

recount3

                   Changes in version 0.99.0                        

NEW FEATURES

• Added a NEWS.md file to track changes to the package.
• Documentation website is now available at http://LieberInstitute.github.io/recount3/. It gets updated with every commit on the master branch (bioc-devel) using GitHub Actions and pkgdown.

recountmethylation

                   Changes in version 0.99.0                        

• Added getdb functions for database file download and load

• Added servermatrix function to get latest database file metadata

• Added User’s Guide and Data Analyses vignettes

• Added metadata and data_analyses.RData to /inst/extdata

                    Changes in version 0.01                         
  

• Added key query/accessor functions.

• Added package vignette.

recoup

             Changes in version 1.17.1 (2020-05-03)                 

NEW FEATURES

• New annotation based on an SQLite database. Rebuild must be performed otherwise the application will break. Download of a ready made annotation is also available (see vignette).

• More supported genomes

• Quick, high-level profile based on RPM instead of coverage

• Speed and code improvements

BUG FIXES

• Fixed bug resulting in running the same operation multiple times when chunking was requested.

RegEnrich

                   Changes in version 0.99.19                       

• Fix bugs in .regSEA function.

                   Changes in version 0.99.18                       
  

• Update R version dependency to 4.0.0.

                   Changes in version 0.99.17                       
  

• Fix bugs of regenrich_diffExpr function.
• Add an example for %>%.

• Use Authors@R [cre] designation.

                   Changes in version 0.99.16                       
  

• Import magrittr

                   Changes in version 0.99.15                       
  

• Fix a bug in regenrich_rankScore function.

• Reexport pipe %>%.

                   Changes in version 0.99.14                       
  

• Add \donttest tags.
• Optimize COEN function.

• Replace bplapply by lapply in pickSoftThreshold2 function.

                   Changes in version 0.99.13                       
  

• Fix bugs of plotSoftPower on Windows.
• Hide documentations of COEN and GRN functions.

• Remove doParallel package from imports.

                   Changes in version 0.99.12                       
  

• Remove .Rpoj file.

                   Changes in version 0.99.11                       
  

• Remove \dontrun tags from all examples.
• Remove lazyData: true from DESCRIPTION.
• Formatting vignettes using BiocStyle.
• Replace NEWS file by NEWS.md file to track changes to the package.
• Some packages in Imports are moved to Depends in DESCRIPTION file.
• DeaSet class inherits SummarizedExperiment class.
• RegenrichSet class inherits DeaSet class.
• TopNetwork class inherits BiocSet class.
• topResult and allResult slots of Enrich object are tibble rather than data frame.
• Score class inherits tibble.

• The show methods for DeaSet, TopNetwork, Enrich, Score, and RegenrichSet object have been optimized.

                   Changes in version 0.99.1                        
  

• Submission to Bioconductor.

regionReport

                   Changes in version 1.23.2                        

SIGNIFICANT USER-VISIBLE CHANGES

• No longer suggest DESeq since this package has been deprecated.

regutools

                    Changes in version 1.1.3                        

SIGNIFICANT USER-VISIBLE CHANGES

• The package CITATION file has been updated now that the online paper on regutools is available at https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btaa575/5861528 with DOI 10.1093/bioinformatics/btaa575 and PMID: 32573705.

DOCUMENTATION UPDATES

• roxygen version update was included and documentation was build under the new roxygen version.

                    Changes in version 1.1.1                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• The package CITATION file has been updated now that the pre-print on regutools is available at https://www.biorxiv.org/content/10.1101/2020.04.29.068551v1 with DOI https://doi.org/10.1101/2020.04.29.068551.

ResidualMatrix

                    Changes in version 1.0.0                        

• New package ResidualMatrix, containing the ResidualMatrix class migrated from BiocSingular.

rfaRm

             Changes in version 1.1.10 (2020-10-13)                 

• Added missing item (alignmentEndPositionQuery) to the output list in the documentation of rfamSequenceSearch

             Changes in version 1.1.9 (2020-10-13)                  
  

• Fixed a bug that caused sequence searches with sequences longer than 10000 bases to crash

             Changes in version 1.1.6 (2020-10-01)                  
  

• Set SSL security level to 1 in Linux environment to bypass a bug in OpenSSL 1.1.1

             Changes in version 1.1.5 (2020-09-30)                  
  

• Reverted changes introduced in 1.1.4

             Changes in version 1.1.4 (2020-09-29)                  
  

• Changed all URLs to http to prevent issues when accessing websites via HTTPS due to a bug in OpenSSL 1.1.1

             Changes in version 1.1.3 (2020-07-18)                  
  

• Fixed a bug that caused sequence searches to crash when applying clan competition filter and no associated clan was found for some Rfam families

             Changes in version 1.1.2 (2020-07-15)                  
  

• Fixed a bug that caused sequence searches to crash when applying clan competition filter and a match was found in the - strand

             Changes in version 1.1.1 (2020-07-08)                  
  

• Added the possibility to filter hits of a sequence search by clan competition

• Sequences larger than 10000 nucleotides can now be provided as input for sequence-based searches of the Rfam database

rGREAT

                   Changes in version 1.21.1                        

• parseRegionGeneAssociationFile(): parsing also considers positions with no sign.

rgsepd

                    Changes in version 1.21                         

• changing some less than signs to less than or equal to, to ensure we get results.

• planning a refactor to handle other gene ID systems and example datasets. not done

rhdf5

                   Changes in version 2.34.0                        

NEW FEATURES

• Added support for read access to files in Amazon S3 buckets (currently only available on non-Windows platforms).

• Included read and write support for dynamic compression filters distributed in rhdf5filters.

CHANGES

• All datasets written with h5write() now have the attribute rhdf5-NA.OK added to them. This is used to indicate that rhdf5 was used to create the file and that the user does not need to be informed that specific values will be mapped to NA in R.

BUG FIXES

• Fix bug in H5Dget_storage_size() where the wrong C function was called.

• NA values in logical datatypes are now preserved when written and read back into R (https://github.com/grimbough/rhdf5/issues/58).

• Fixed error when trying to write a vector containing only empty strings (https://github.com/grimbough/rhdf5/issues/60).

• h5ls() and h5dump() no longer crash when given a file containing recursive or duplicated groups (https://github.com/grimbough/rhdf5/issues/48).

• Reading compound datasets with at least one 8-bit integer field now works (https://github.com/grimbough/rhdf5/issues/71).

• Fixed problem when writing a data.frame containing a column of raw values. These columns were ommitted when creating a compound dataset.

• Patch early UNPROTECT() when reading a Enum type that could cause a segmentation fault (https://github.com/grimbough/rhdf5/issues/73)

rhdf5filters

                    Changes in version 1.2.0                        

BUG FIXES

• Now passed R CMD config LDFLAGS to the compilation of the BLOSC filter.

ribosomeProfilingQC

                    Changes in version 1.1.6                        

• fix the issue in shiftReads for reads width and readsEndPlot for seqlevels.

                    Changes in version 1.1.5                        
  

• Update documentation about the R version requirement.

                    Changes in version 1.1.4                        
  

• Update authorship.

                    Changes in version 1.1.3                        
  

• Fix the error “CIGAR is empty after qnarrowing”.

                    Changes in version 1.1.2                        
  

• update vignette to fix the typos.

• update plotTranscript to give more informative warning message.

                    Changes in version 1.1.1                        
  

• update vignette by adding background colors for better understanding the pipeline.

RNAAgeCalc

             Changes in version 1.1.2 (2020-09-20)                  

• Added citation and README

             Changes in version 1.1.1 (2020-06-24)                  
  

• Replaced “DESeq” with “DESeq2” throughout the package

rnaEditr

                   Changes in version 0.99.1                        

2020-10-01

Added rnaEditr.Rproj into .gitignore to fix the building error.

                   Changes in version 0.99.0                        

2020-09-22

We are planning to submit to Bioconductor by this Friday, and here is the link to the issue on gitlab where we resolve BiocCheck() ERRORs, WARNINGs, and NOTEs: https://gitlab.com/Jennyzly2016/rnaEditr/-/issues/64

RNAmodR

             Changes in version 1.3.5 (2020-08-30)                  

• bugfix for GRangesList as annotation data. Only non-overlapping elements are allowed

             Changes in version 1.3.1 (2020-04-29)                  
  

• added stats function to access details about number of reads used for analysis

RnaSeqSampleSize

             Changes in version 1.99.2 (2020-10-22)                 

BUG FIXES

• Change codes to make the package pass all Rcmd check with R 4.0.3

RnBeads

                    Changes in version 2.7.1                        

• Added conversion from RnBeadRawSet to RGChannelSet

rols

                    Changes in version 2.17                         

CHANGES IN VERSION 2.17.4

• Fix failing unit test <2020-08-26 Wed>

CHANGES IN VERSION 2.17.3

• Fix failing unit test (Matched error messsage changed) <2020-07-01 Wed>

CHANGES IN VERSION 2.17.2

• Fix failing unit test (Terms changed) <2020-06-09 Tue>

CHANGES IN VERSION 2.17.1

• Fix failing unit test (GO description changed) <2020-05-01 Fri>

CHANGES IN VERSION 2.17.0

• Bioconductor devel version (Bioc 3.12)

ROSeq

                   Changes in version 1.99.01                       

• no bug, but removed extra files from man folder

                   Changes in version 1.1.12                        
  

• updated vignettes and readme file and example in main file
• Publication (Preprint available at BioRxiv): is added

rrvgo

                    Changes in version 1.1.3                        

• Warn user when no scores are provided and thus falling back to term’s size as the score to rank terms

                    Changes in version 1.1.2                        
  

• Fix bug that would break reduceSimMatrix() when no scores were provided

rScudo

                    Changes in version 1.5.1                        

USER VISIBLE CHANGES

• Updated citation

• An error is returned if there are duplicated sample names in the expression data

rsemmed

                   Changes in version 0.99.0                        

• Initial release to Bioconductor

Rsubread

                    Changes in version 2.4.0                        

• The ‘isPairedEnd’ parameter in featureCounts() is now used to check if the type of input reads (paired-end or single-end) is correctly specified.

• A new parameter ‘countReadPairs’ was added to featureCounts to specify if read pairs should be counted for paired-end read data.

• Changes to the input parameters and output of cellCounts() function. CellCounts will generate a Sample Sheet for samples included in the scRNA-seq data, based on the sample index set name provided by the user. Structure of the List object returned by cellCounts() is also simplified. cellCounts() now also outputs a BAM file and a gzipped FASTQ file including raw reads for each sample.

RTCA

                 Changes in version 2009-07-13                      

• combineRTCA(list): Additional column is renamed into Plate. The vlues is evaluated from list item names. When the list has no name, an integer index beginning from 1 is used. Special attentions to list partially with names is noted in the documentation.

• parseRTCA(file, dec=”.”,phenoData, skipWell,…): Example is added in the documentation how to import pre-configured phenoData. Details section in the documentation is re-written to describe the process of parsing.

• RTCA-class: Experiment ID added to RTCA class

• Makefile: add Makefile to simplify common tasks like check and install

• plotGridEffect: takes ‘column’ instead of ‘col’ as mode parameter, and renders the mode as the title of the legend. Documentation updated.

• plotRTCA: is removed from the package and is substituted by the plot function.

RTCGAToolbox

                   Changes in version 2.20.0                        

New features

• Added the RNASeq2Gene slot to the FirehoseData class. This data type mainly obtains RNASeq v2 raw_counts from the pipeline (scaled_estimates also available; @mherberg #39)
• Added an accmini example dataset as obtained from getFirehoseData
• getLinks function shows the user some file provenance based on data requested
• Newly deprecated functions: getDiffExpressedGenes, getCNGECorrelation, getSurvival and getReport. It is no longer possible for the maintainer to update these functions in a way that would benefit users. A transfer of responsibility would be required, i.e. to another package.
• Vignettes are updated to reflect changes in the codebase.

Bug fixes and minor improvements

• Improvements to internal functions for converting tabular data to Bioconductor classes
• Missing (NA) seqnames are removed when converting to RaggedExperiment
• Remove static file dependencies from GitHub and use text inside function (@DavisWeaver, #34)
• Added default values to helper for making SummarizedExperiment datasets
• Coerce sample names to character when in (the rare) case they’re numeric
• Added an ellipsis argument to biocExtract for specifying the names.field in tabular data that will correspond to the row names of a SummarizedExperiment

Rtpca

             Changes in version 0.99.2 (2020-06-05)                 

• Submitted to Bioconductor

rWikiPathways

                   Changes in version 1.10.0                        

• Defuncted getColoredPathway

• Doc fix: examples fixed and sample gmt included

                    Changes in version 1.8.5                        
  

• Doc fix: added reference to clusterProfiler

                    Changes in version 1.8.4                        
  

• Doc fix: fixed Pathway Analysis vignette

                    Changes in version 1.8.3                        
  

• Bug fix: GMT parsing #16

                    Changes in version 1.8.2                        
  

• Doc fix: vignette with BridgeDbR

• Bug fix: fixed rjson replacement

S4Vectors

                   Changes in version 0.28.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Replaced DataTable class with RectangularData class.

• Replaced DataTable_OR_NULL with DataFrame_OR_NULL class.

• Add parallel_slot_names() generic and methods for Vector derivatives. This replaces vertical_slot_names(). The concept of “vertical” and “horizontal” slots is now a RectangularData concept only i.e. only RectangularData derivatives should define vertical_slot_names() and horizontal_slot_names() methods. For RectangularData derivatives that are also Vector derivatives, one of the two methods should typically be defined as a synonym of parallel_slot_names(). For example horizontal_slot_names() now returns parallel_slot_names() on a DataFrame derivative and vertical_slot_names() will return parallel_slot_names() on a SummarizedExperiment derivative.

• makeClassinfoRowForCompactPrinting() is now exported.

• showAsCell() now trims strings that are > 22 characters.

• Small tweak to show() method for Rle objects. Now it uses showAsCell() instead of as.character() for more compact display of the run values of the Rle object, and for consistency with other show() methods (e.g. with method for DataFrame objects).

DEPRECATED AND DEFUNCT

• parallelSlotNames() is now defunct (after being deprecated in BioC 3.11).

BUG FIXES

• Fix coercion from SimpleList to DataFrame.

• Fix bug in showAsCell() on ordinary data frames.

• Make sure showAsCell() works on a list of non-subsettable objects.

SAIGEgds

                    Changes in version 1.3.3                        

• set-based tests: burden, ACAT-V

                    Changes in version 1.2.2                        
  

• update the citation

• work around gcc-10

sangeranalyseR

                   Changes in version 0.99.1                        

• Base class: SangerReads is designed to store each forward/revers reads.

                    Changes in version 0.1.0                        
  

• Project starts.

SCATE

                    Changes in version 1.0.0                        

• submission to Bioconductor

scCB2

                   Changes in version 0.99.31                       

• Added extra filtering for barnyard data (a mixture of multiple species).

                   Changes in version 0.99.30                       
  

• Added thresholding of number of top genes to use in testing steps. This avoids high number of false positives in ultra-high dimensional datasets, e.g. 10x barnyard data.

                   Changes in version 0.99.29                       
  

• Updated functions of calculating Pearson correlation in sparse matrix. New functions are more accurate.

                   Changes in version 0.99.25                       
  

• Changed R dependency back to 4.0.0.

                   Changes in version 0.99.24                       
  

• Removed direct download files in vignettes to speed up building.
• Changed R dependencies so that package can be built in older R versions.

• Changed vignette title to match the citation.

                   Changes in version 0.99.23                       
  

• Minor edit of README.md

                   Changes in version 0.99.22                       
  

• Received comments from Bioconductor reviewer.
• Moved BiocStyle from Imports: to Suggests:.
• Modified vignettes. Deleted GitHub installation instruction.
• Changed default value of Ncores to be 2.

• Changed output of CB2FindCell to be an SummarizedExperiment object. Changed GetCellMat accordingly. Changed examples and testthat accordingly.

                   Changes in version 0.99.21                       
  

• Updated testthat scripts.

• Minor bug fix in Read10xRaw.R. Added as.numeric when building sparse matrix.

                   Changes in version 0.99.20                       
  

• Updated citation.

                   Changes in version 0.99.19                       
  

• Minor edits on package vignettes.

                   Changes in version 0.99.18                       
  

• Minor bug fix.

• Minor edits on package vignettes.

                   Changes in version 0.99.17                       
  

• Initial version preparing to submit to Bioconductor.

                   Changes in version 0.99.16                       
  

• Change function name Read10X to be Read10xRaw, Read10Xh5 to be Read10xRawH5.
• Change parameter name PrintProg to be verbose.
• Minor edits on parameter description of function GetCellMat.

• Added a quick function QuickCB2 by combining all necessary functions into one. Input: directory of raw data. Output: filtered matrix, or a Seurat object containing filtered matrix.

                   Changes in version 0.99.15                       
  

• When dividing barcodes into groups with similar barcode counts, the last group will be combined with second last group if the number of barcodes in the last group is less than half of that in the second last group.

                   Changes in version 0.99.14                       
  

• Change parameter names to match those in the paper: retain -> upper. background -> lower.

                   Changes in version 0.99.13                       
  

• Rounded baseline threshold.
• Minor changes on vignette.

• Bug fix when retain threshold is larger than any barcode.

                   Changes in version 0.99.12                       
  

• Minor changes on vignette.

• Baseline (2 * background) clustering threshold will be printed out.

                   Changes in version 0.99.11                       
  

• Customized knee point calculation function.
• CB2FindCell will print out retain threshold in standard output.

• Minor bug fixes when there is no cluster.

                   Changes in version 0.99.0                        
  

• Created initial github page.
• Created package.
• Created vignettes.
• Checked package… passed R CMD check and BiocCheck.
• Ready to submit to Bioconductor.

scDataviz

                    Changes in version 1.0.0                        

• Submitted to Bioconductor

scDblFinder

             Changes in version 1.3.25 (2020-10-26)                 

• scDblFinder has important improvements on speed, robustness and accuracy

• in additional to doublet calls, scDblFinder reports the putative origin (combination of clusters) of doublets

             Changes in version 1.3.19 (2020-08-06)                 
  

• scDblFinder now hosts the doublet detection methods formerly part of scran

scDD

             Changes in version 1.13.1 (2020-08-17)                 

• When testing for difference in proportion of zeroes, if the Bayesian logistic regression fails to converge for a given gene (for example, if there is perfect separation between conditions), then NA will be returned (instead of throwing an error.

SCFA

             Changes in version 0.99.0 (2020-08-13)                 

• Submitted to Bioconductor

scp

                    Changes in version 0.99                         

scp 0.99.4

• Update installation instructions <2020-10-14 Wed>

scp 0.99.3

• fix: solved ‘invalid subsetting’ issue <2020-10-14 Wed>
• Adapted the vignette to remove warnings and fix missing PCA plot. <2020-10-14 Wed>
• README.md: extended the installation guide, providing both a stable and a devel installation. <2020-10-13 Tue>
• Removed the LazyLoad from the DESCRIPTION file and adapted the data loading (eg data(scp1) to data(“scp1”)) <2020-10-13 Tue>
• Documentation: added data collection description for the 3 example datasets <2020-10-13 Tue>

scp 0.99.2

• fix: computeFDR can handle missing values (see issue #12) <2020-10-02 Fri>

scp 0.99.1

• Maintainer subscribed to bioc-devel mailing list
• Removed infIsNA, the implementation was moved to the QFeatures packages

scp 0.99.0

• Bioconductor submission

scPCA

             Changes in version 1.3.10 (2020-10-16)                 

• Implementing suggested improvements from Aaron Lun

             Changes in version 1.3.9 (2020-10-12)                  
  

• scPCA now accepts DelayedMatrix objects as target and background datasets.

             Changes in version 1.3.8 (2020-09-01)                  
  

• Minor bug fixes

             Changes in version 1.3.6 (2020-08-30)                  
  

• Fixed issue where n_centers was required when only one penalty and contrast term were provided

• Users can now pass factors and character vectors to the clusters argument.

             Changes in version 1.3.5 (2020-08-18)                  
  

• Fixed citations in docs
• Provided more detailed warning when RSpectra::eigs_sym fails to converge

• Included argumetns in scPCA to control RSpectra::eigs_sym convergence: error tolerance and max number of iterations

             Changes in version 1.3.4 (2020-08-12)                  
  

• Replaced calls to base::eigen by RSpectra::eigs_sym to speed up eigendecompositions of contrastive covariance matrices. cPCA is now performed much more quickly when only whishing to compute a handful of leading contrastive principal components.
• Replaced calls to stats::cov by coop::covar to speed up computation of large sample covariance matrices.

• In future updates, we’d like to explore using the DelayedArray framework to support the analysis of larger datasets.

             Changes in version 1.3.3 (2020-08-08)                  
  

• The n_centers argument no longer matters when When the contrasts argument is of length 1 and the penalty term is set to 0.

• Users can now pass in their own cluster labels

             Changes in version 1.3.2 (2020-08-05)                  
  

• Updated scPCA function documentation
• Corrected pelling mistakes

scran

                   Changes in version 1.18.0                        

• Deprecated coassignProbs() as this is replaced by bluster::pairwiseRand()

• Deprecated boostrapCluster() as this is replaced by bluster::bootstrapStability().

• Deprecated gene.names= in the various pairwise* functions as being out of scope.

• Added the testLinearModel() function to obtain inferences from a linear model.

• Modified pseudoBulkDGE() to use formulas/functions in the design= argument. Allow contrast= to be a character vector to be run through makeContrasts().

• Added the pseudoBulkSpecific() function to test for semi-label-specific DEGs in pseudo-bulk analyses.

• Added the summaryMarkerStats() function to compute some basic summary statistics for marker filtering.

• Modified row.data= in findMarkers() to support list inputs. Added a add.summary= option to easily include summary information.

• Modified combineVar() and combineCV2() to support list inputs.

• Deprecated doubletCells() as this is replaced by scDblFinder::computeDoubletDensity().

• Deprecated doubletCluster() as this is replaced by scDblFinder::findDoubletClusters().

• Deprecated doubletRecovery() as this is replaced by scDblFinder::recoverDoublets().

• Added sparse-optimized variance calculations to modelGeneVar(), modelGeneCV2() and related functions, which may result in slight changes to the results due to numeric precision.

• Exported combineBlocks() to assist combining of block-wise statistics in other packages.

• Added lowess= and density.weights= options to fitTrendVar() to rescue overfitted curves.

• Raised an error in denoisePCA() upon mismatches in the matrix and technical statistics.

scRepertoire

                    Changes in version 1.2.3                        

• Changed the access of the sample data to github.io repo: readRDS(url(“https://ncborcherding.github.io/vignettes/scRepertoire_example.rds”))

                    Changes in version 1.2.2                        
  

• Removed Startrac-based functions in order to pass build on Bioconductor. DEPRECATED AND DEFUNCT

• Deprecate StartracDiversity()

                    Changes in version 1.2.0                        
  

SUBMITTED

• The first version of scRepertoire submitted to Bioconductor.

SIGNIFICANT USER-VISIBLE CHANGES

• Added support for SingleCellExperiement format.

DEPRECATED AND DEFUNCT

• Deprecate combineSeurat in favor or combineExpression().

• Deprecate seurat2List in favor of expression2List().

                   Changes in version 0.99.18                       
  

• Updated author information in the vignette

                   Changes in version 0.99.17                       
  

• Updated NEWS formatting

• Edited DESCRIPTION to SingleCellExperiment R package

• Updated information in the vignette

                   Changes in version 0.99.16                       
  

• Added getCirclize()

                   Changes in version 0.99.15                       
  

• Modified numerator for index function

                   Changes in version 0.99.14                       
  

• Removed bracket from indexing function

                   Changes in version 0.99.13                       
  

• Added exportTable to remaining viz functions

• Modified morisita index to correct error

                   Changes in version 0.99.12                       
  

• Reducing the size of the screp_example to fulfill < 5 mB requirement. Randomly samples 100 cells and removed RNA counts from Seurat object

                   Changes in version 0.99.11                       
  

• Updated compareClonotype to allow for clonotype comparisons

                   Changes in version 0.99.10                       
  

• Bioconductor did not detect the version update.

                   Changes in version 0.99.9                        
  

• Bioconductor had no love - changed the Seurat package to imports instead of required, see if that will address the compiling issue that results in a killed: 9 error.

                   Changes in version 0.99.8                        
  

• Passed checks on system, let’s see how much bioconductor hates it

                   Changes in version 0.99.7                        
  

• But really this time, changed the colData import

                   Changes in version 0.99.6                        
  

• Changed colData import

                   Changes in version 0.99.5                        
  

• Added screp_example data to package

• Added visVgene function for visualizing the distribution of V genes in TCR

• Added support for monocle to combineExpression function

• Updated documentation for combineTCR() and combineBCR()

• Updated documentation to utilize SingleCellExperiment formats

• Updated Vignette to utilize SingleCellExperiment formats

• Added Author information to vignette

• Add intro and conclusion to vignette

• Removed html knitted vignette

• Removed descriptive code snippets

                   Changes in version 0.99.4                        
  

• Modified expression2List() to allow for variables across meta data

                   Changes in version 0.99.1                        
  

• Changed R (>= 3.6) to R (>= 4.0)

                   Changes in version 0.99.0                        
  

• Changed DESCRIPTION version to 0.99.0

• Removed file seurat_example.rda, accidentally committed

• Deleted git attributes

• reduced Seurat object size for alluvialClonotype in vignette

• Changed the alluvialClonotype assessment to account for only 1 condition

scTensor

                    Changes in version 2.0.0                        

• Extended to use the version 2.0.0 of LRBase.XXX.eg.db-type packages

• Omitted typing Enter-key many times to perform example(‘cellCellReport’)

• lr.evidence option was added in cellCellRanks() and cellCellDecomp() to select ligand-receptor databases to construct CCI-tensor (cf. Evidence code: https://github.com/rikenbit/lrbase-workflow)

• The L-R evidence was embeded in the HTML report.

• The bug related to the hyper-link was fixed in .hyperLinks.

• Auto library installation/loading for MeSH.XXX.eg.db. Note that this function is based on the NCBI Taxonomy ID embedded in METATDATA table in the sqlite3 file of LRBase.XXX.eg.db.

• The order of the parameters of cellCellSetting were changed as cellCellSetting(sce, lrbase, label, lr.evidence=”all”, color=NULL), and color parameter was changed as a optional parameter. If it is not specified, the color is automatically selected.

• The way to specify the celltype label was changed in cellCellSetting.

• The vignettes were modified.

• The convertNCBIGeneID is deprecated. The same functionality can be available as scTGIF::convertRowID instead.

                   Changes in version 1.4.1-3                       
  

• A bug was fixed in .cellCellDecomp.Halpern()

scTGIF

                    Changes in version 1.2.1                        

• A bug is fixed in convertRowID()

scuttle

                    Changes in version 1.0.0                        

• Split off scuttle from scater by migrating all non-visualization code from the latter.

• Began transition to dot-separate argument names from original snake case format.

• Added a geometricSizeFactors() function, deprecated geometric=TRUE in librarySizeFactors().

• Single-object downsampling in downsampleBatches() now behaves more consistently with multi-object downsampling.

SDAMS

                    Changes in version 1.9.2                        

• update description for single-cell data in reference manual.

                    Changes in version 1.9.1                        
  

• add example for single-cell data.

semisup

             Changes in version 1.14.0 (2020-05-05)                 

• Updated documentation

SeqArray

                   Changes in version 1.29.2                        

UTILITIES

• show a warning when an unsorted index is used in seqSetFilter()

• show a message if seqVCF_Header() fails

• a new option ‘chr_prefix’ in seqGDS2VCF()

BUG FIXES

• seqVCF_Header() fixes ‘contig’ in the header of VCF if there are different fields

                   Changes in version 1.28.1                        
  

BUG FIXES

• seqRecompress(, verbose=FALSE) works correctly

• seqSetFilter(, action="push+set") should not reset the filter before setting a new filter

SeqGate

             Changes in version 0.99.3 (2020-09-18)                 

• Updated vignette and documentation regarding SummarizedExperiment

• Updated NAMESPACE regarding SummarizedExperiment

             Changes in version 0.99.2 (2020-09-08)                 
  

• Changed code to take SummarizedExperiment objects as input and output

• Changed tests for this new code

             Changes in version 0.99.1 (2020-09-01)                 
  

• Added BugReports field to the DESCRIPTION file

• Fixed typo in checkForReplicates function name

• Replaced cat by message, warning or stop

• Suppressed unappropriate keywords (e.g., ERROR, WARNING) in messages

• Replaced external datasets by generated datasets in tests

• Suppressed rm(list=list()) in tests

             Changes in version 0.99.0 (2020-07-09)                 
  

• Submitted to Bioconductor

seqLogo

                   Changes in version 1.55.2                        

NEW FEATURES

• Added accessor function to access pwm, ic and consensus

• Added possibility to specify colors (by setting fill)

• Added support for RNA logos

BUG FIXES

• Replaced class statements with is(..., "class")

SeqVarTools

                   Changes in version 1.27.1                        

• Add ‘parallel’ argument to methods.

sevenbridges

                   Changes in version 1.19.2                        

Improvements

• Transfer package maintainership.

                   Changes in version 1.19.1                        
  

Bug Fixes

• Fixed an API issue on invalid JSON when running tasks.
• Fixed a subtle column class mismatch issue when binding data frames since R 4.0.0.

Improvements

• Use data.table::rbindlist() when possible to increase the data frame binding performance.

SharedObject

                   Changes in version 1.3.18                        

• Make the package functions process-safe

                    Changes in version 1.3.8                        
  

• Support complex

• Support pairlist

• Use memcpy to copy the data when possible

                    Changes in version 1.3.7                        
  

• change the parameters of is.shared function

• mustWork = FALSE by default, no error will be given when sharing a nonsharable object

• Support environment object

                    Changes in version 1.3.6                        
  

• Support S4 object

• new dispatching method(signiture “ANY”) for share, unshare and is.shared functions

ShortRead

                    Changes in version 1.48                         

NEW FEATURES

• (v 1.47.1) countFastq() counts the number of records, nucleotides, and quality scores in one or several fastq files.

signatureSearch

             Changes in version 1.2.4 (2020-08-14)                  

• Supported defining gene set database from score matrix by setting higher, lower, as well as padj cutoffs for gCMAP and Fisher GESS methods

             Changes in version 1.2.2 (2020-07-11)                  
  

• Supported converting gmt file to HDF5 file (01 matrix) as gene set reference database for gCMAP and Fisher GESS methods

simplifyEnrichment

                   Changes in version 0.99.5                        

• in the clustering, considered when the size of cluster is only 1.

• add partition_by_kmeanspp().

• col can be set as a vector of colors.

                   Changes in version 0.99.4                        
  

• support more ontologies.

• support to calculate similarity matrix by gene overlap.

• node partition fun changed to pam

SingleCellExperiment

                   Changes in version 1.12.0                        

• Added the rowSubset() function as a standard location for a row subset.

• Added colPairs() and rowPairs() to store pairwise information (e.g., for graphs).

• Added method specifications for S4Vectors compatibility.

singleCellTK

             Changes in version 2.0.0 (2020-10-16)                  

• Added quality control (empty droplet detection, doublet detection, etc) functionality

• Ability to import data from varying preprocessing tools

• Ability to export SingleCellExperiment object as varying file types (flat file, Python anndata)

• Added functions for visualization of data

• New CellViewer functionality in UI

• Improvements to differential expression, now includes DESeq2, limma, ANOVA

• Incorporates Seurat workflow

SingleR

                    Changes in version 1.4.0                        

• Migrated all of the dataset getter functions to the celldex package.

• Streamlined the vignette to point to the book at <URL: http://bioconductor.org/books/devel/SingleRBook/>.

• Added a restrict= argument to trainSingleR() and SingleR() to easily restrict to a subset of features.

• Deprecated the method= argument in SingleR().

• Protect against accidental data.frames in ref= or test= in all functions.

sitePath

                   Changes in version 1.5.25                        

• Bug fix: use ‘geom_point2’ instead of ‘geom_tippoint’ to avoid error.

                   Changes in version 1.5.24                        
  

• Add sequence type option for for DNA and amino acid.

• Deprecate ‘multiFixationSites’ function.

• Use ‘y’ argument as mutation label option in ‘plot.sitePath’ function.

• Finer lineage resolving method used in ‘lineagePath’ function.

                   Changes in version 1.5.23                        
  

• Create ‘groupTips’ functions to replace ‘as.list’ functions for ‘fixationSites’ and ‘fixationPath’ object.

• Create ‘sitesMinEntropy’ function to output raw result of entropy minimization.

• Create ‘parallelSites’ function and other functions for its return object such as ‘plotSingleSite’ and ‘as.data.frame’

                   Changes in version 1.5.22                        
  

• Fix missing newline when printing ‘phyMSAmatched’ object.

• Create ‘as.list.fixationSites’ for retrieving grouped tips.

• Remove ‘tipname’ option in ‘as.data.frame.fixationSites’.

                   Changes in version 1.5.21                        
  

• Fix wrong group name in some corner cases.

• Use ‘ggtree’ for ‘plotSingleSite’.

                   Changes in version 1.5.20                        
  

• Further fix the merging issue in ‘fixationSites’.

                   Changes in version 1.5.19                        
  

• Speed up ‘SNPsites’.

                   Changes in version 1.5.18                        
  

• Bifurcation check for the phylogenetic tree and force bifurcation.

• Fix path merging issue in ‘fixationSites’.

                   Changes in version 1.5.17                        
  

• Import ‘aes’ and ‘theme’ from ‘ggplot2’.

                   Changes in version 1.5.16                        
  

• Allow turning off mutation label for ‘plot.fixationSites’ while legend of cluster name becomes compulsory.

• Import ‘scale_color_manual’ from ‘ggplot2’.

• Update vignette.

                   Changes in version 1.5.15                        
  

• Bug fix: NA in cluster name.

                   Changes in version 1.5.14                        
  

• Add ‘as.treedata’ function for ‘fixationSites’.

                   Changes in version 1.5.13                        
  

• Hierarchical naming of the clusters.

                   Changes in version 1.5.12                        
  

• Establish ‘phyMSAmatched’ S3 class for better encapsulation.

                   Changes in version 1.5.11                        
  

• Deprecate ‘multiFixationSites’ function.

                    Changes in version 1.5.8                        
  

• Wrap mutations text in ‘plot.fixationSites’.

• Remove ‘color’ argument for ‘plot.fixationSites’ as the number of groups is usually unknown.

                    Changes in version 1.5.7                        
  

• Left padding with 0 for the cluster name.

• Add mutation label when plot ‘fixationSites’.

• Add ‘as.data.frame’ function for ‘fixationSites’.

                    Changes in version 1.5.6                        
  

• Add ‘sitewiseClusters’ function and plot function for its visualization.

                    Changes in version 1.5.5                        
  

• Add ‘plotMutSites’ function to visualize mutations of each tree tip.

                    Changes in version 1.5.4                        
  

• Use ‘ggtree’ for ‘plot.lineagePath’.

• More informative plot for ‘sneakPeek’ and add ‘lineagePath’ function for its return.

                    Changes in version 1.5.3                        
  

• Add ‘as.phylo.fixationSites’ function that represent site fixations as simplified phylgenetic tree.

                    Changes in version 1.5.2                        
  

• Add ‘minEffectiveSize’ in ‘plot.fixationSites’ for filtering small sized tip clusters.

                    Changes in version 1.5.1                        
  

• Add ‘plot.fixationSites’ function.

                    Changes in version 1.4.1                        
  

• Fix: broken link in the DESCRIPTION.

snifter

             Changes in version 0.99.0 (2020-07-17)                 

• First version of the package.

SNPRelate

                   Changes in version 1.24.0                        

• definition of IBS in the snpgdsIBS help file

sparseMatrixStats

             Changes in version 1.0.5 (2020-05-17)                  

• Fix links in documentation to get rid of WARNINGS

             Changes in version 1.0.4 (2020-05-17)                  
  

• Fix bugs in colTabulates

• Update documentation to avoid warnings in build on Windows

             Changes in version 1.0.3 (2020-05-17)                  
  

• Fix bug in colAnys and colAlls if value = TRUE

             Changes in version 1.0.2 (2020-05-10)                  
  

• Fix bug in colMaxs, colMins related to missing values

             Changes in version 1.0.1 (2020-05-08)                  
  

• Fix bugs in colMaxs, colMins, colAnys

• Fix bug in colLogSumExps

SparseSignatures

                    Changes in version 2.0.0                        

• Migration from Travis-CI to Github Actions.

• Major refactoring.

SpatialDecon

             Changes in version 0.99.0 (2020-10-02)                 

• Submitted to Bioconductor

spatialHeatmap

             Changes in version 0.99.0 (2020-09-21)                 

• Submitted the first version to Bioconductor

Spectra

                    Changes in version 0.99                         

Changes in 0.99.11

• Re-add mz and intensity as core spectra variables.

Changes in 0.99.10

• Fix in spectraData<-,Spectra to avoid removing m/z and intensity values (issue #146).
• Add default implementations of filter functions for MsBackend.

Changes in 0.99.9

• Fix in Spectra,character constructor to ensure the backend is changed even if source inherits from backend (issue #143).

Changes in 0.99.8

• combineSpectra applies data processing steps in the processing queue prior to combination (issue #140).

Changes in 0.99.7

• Fix problem in dropNaSpectraVariables that would also drop m/z and intensity values for most backends (issue #138.

Changes in 0.99.6

• Support intensity in filterIntensity method to be a function to enable peak intensity-based filtering of spectra (issue #126).

Changes in 0.99.5

• Add filterMzRange and filterMzValues to filter spectra based on an m/z range or a list of target m/z values, respectively.

Changes in 0.99.4

• Add export,MsBackendMzR to export spectra data to mzML or mzXML file(s).
• Add an export,MsBackend method to allow backends to take care of data export.
• Refactor export,Spectra to use the MsBackend class to export the data.
• Change parameter source in Spectra,character to MsBackendMzR and set parameter backend = source. Thus by default, the import backend will also be used to store the data.

Changes in 0.99.3

• Replace lapply,Spectra with spectrapply,Spectra.

Changes in 0.99.2

• Replace asDataFrame,MsBackend with spectraData,MsBackend.
• Replace asDataFrame<-,MsBackend with spectraData<-,MsBackend.
• Replace as.list,MsBackend with peaksData,MsBackend.
• Replace replaceList<-,MsBackend with peaksData<-,MsBackend.
• Replace as.list,Spectra with peaksData,Spectra and add methods to coerce a Spectra to a list or SimpleList.

Changes in 0.99.0

• Add reset method.
• Add processing by chunk to compareSpectra.

splatter

             Changes in version 1.14.0 (2020-10-28)                 

• Add the splatPop simulation. This is a extension to the splat simulation contributed by Christina Azodi and Davis McCarthy that adds population effects. It allows you to specify relatedness between individuals and generate cell-type specific eQTL effects.

• Add a batch.rmEffect parameter to the Splat simulation. This allows generation of a paired simulation without any batch effects.

• Add a new minimiseSCE function which can be used to remove unneeded information from simulation output (or any SingleCellExperiment)

• All simulations now return sparse assay matrices by default when they would be smaller than the equivalent dense matrix. This is controlled by a new sparsify argument.

• Users will now be automatically prompted to install packages if they try to use a simulation for which the suggested dependencies are not available

splineTimeR

             Changes in version 1.17.1 (2020-07-18)                 

• Fixed bug. Limit for counter of inner loop in function splinePlot corrected

• Signigicant changes o Log output to console in function splinePlot o package NEWS file added

SPsimSeq

                   Changes in version 0.99.0                        

• First private GitHub document
• Major revision including gene/featurewise dependence
• Minor revision on documentation and adding new features
• Optimizing outputs, further enhancement, fixing bugs, and addressing issues
• Added unit tests

statTarget

                     Changes in version 2.0                         

NEW FEATURES

• New GUI o Mouse Hover for help information o .log file

• New Signal correction o Combat for QC-free Signal correction o QC-RFSC methods for metabolomics and proteomics data

• New feature slection o Random Forest and the Permutation based variable importance measures o new MDSplot for Random Forest o P-value based importance plot

• New data preprocessing o PQN/SUM/none normalization o center/none Scaling method

                   Changes in version 1.19.1                        
  

• To fixed bugs for coCV function

struct

                    Changes in version 1.1.2                        

• improved ‘show’ output for objects

• allow ANY for entities

                    Changes in version 1.1.1                        
  

• added citations slot to struct classes

• added corresponding citations method

• added method to get/set seq_in slot

• as.SummarizedExepriment now works correctly

• using seq_in now works for sequences with more than 2 steps

structToolbox

                    Changes in version 1.1.2                        

• Documentation updates

• Bug fixes

                    Changes in version 1.0.1                        
  

• Fix HCA bug

SummarizedExperiment

                   Changes in version 1.20.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• SummarizedExperiment now depends on the MatrixGenerics package.

• DelayedArray was moved from Depends to Imports.

DEPRECATED AND DEFUNCT

• Deprecated readKallisto().

BUG FIXES

• Avoid triggering copies of the assays in assays() getter.

• Fix long-standing bug in dim() method for Assays objects.

• Fix assays(x) <- SimpleList(). Before that fix this operation was turning SummarizedExperiment object (or derivative) ‘x’ into an invalid object.

SWATH2stats

                   Changes in version 1.19.3                        

UPDATE

• Add link to website

                   Changes in version 1.19.2                        
  

BUG FIXES

• remove grid from Description

                   Changes in version 1.19.1                        
  

NEW FEATURES

• validate_columns

update

• update documentation to roxygen2 (many thanks to Ashton Trey Belew (abelew) for starting this and doing most of the work) (IS#1, PR#2, PR#3)

• Some parameters were renamed to omit having a dot. E.g. rm.decoy is now called rm_decoy. If you want the previous names use SWATH2stats up to version 1.19.0

                   Changes in version 1.19.0                        
  

NEW FEATURES

• SWATH2stats in BioC 3.12 development release

TADCompare

            Changes in version 0.99.35 (2020-05-15)                 

• Proper formatting of the NEWS file

            Changes in version 0.99.33 (2020-04-27)                 
  

• Submitted to Bioconductor

TargetSearch

                   Changes in version 1.46.0                        

NEW FEATURES

• New function ri_data_extract to extract peaks from RI files. It works similar to FindAllPeaks but uses different (simpler) input parameters, comparable to ncdf4_data_extract.

• New function ri_plot_peak to plot peaks from RI files, built upon ri_data_extract. It can be used as an alternative to plotPeakRI as it has a simple interface.

• New function ncdf4_plot_peak. An alternative to function plotPeakSimple with a simple interface to plot peaks from NetCDF format 4. This function supersedes plotPeakSimple.

BUG FIXES

• Remove unneeded ICO file.

• Man pages improvements. Mostly grammar and spelling changes.

SIGNIFICANT USER-VISIBLE CHANGES

• The function peakPlotSimple is considered deprecated, and its use should be avoided. Use the function ncdf4_plot_peak instead.

• The parameter column in many columns is now NULL by default. To change the column names use the global option TS_RI_columns instead

TCC

                   Changes in version 1.29.1                        

• delete ‘deseq’ option, since DESeq is deprecated and will be removed from Bioconductor

TCGAutils

                   Changes in version 1.10.0                        

New features

• correctBuild attempts to provide the official name of a particular human genome build to agree with changes in GenomeInfoDb
• isCorrect checks that the build name matches the official name

Minor changes and bug fixes

• Documentation improvements to simplifyTCGA
• Improvements to findGRangesCols to locate ranged columns in a DataFrame
• Fixed a bug in UUIDtoBarcode where only the first record was returned (#26, @DarioS)
• Fixed a bug in filenameToBarcode when multiple inputs were used (#22, @DarioS)

tofsims

                    Changes in version 099.1                        

SIGNIFICANT USER-VISIBLE CHANGES

• changed function behvaiour in the whole package from call-by-ref to call-by value. Adjusted accordingly all examples and the vignette.

INTERNALS

• depends now on ProtGenerics from which it uses ‘mz’

• exchanged various print() with message()

tomoda

             Changes in version 0.99.0 (2020-09-15)                 

• Submitted to Bioconductor

topconfects

                    Changes in version 1.5.3                        

• Small tweaks to better display weitrix_confect outputs.

• Less digits when print()ed.

                    Changes in version 1.5.2                        
  

• nest_confects now copes with NA p-values.

                    Changes in version 1.5.1                        
  

• Fix limits calculation for confects_plot.

ToxicoGx

                    Changes in version 1.1.0                        

• Continue to abstract functionality into CoreGx
• Add additional plotting functions such as grouped boxplots
• Extend coverage of unit tests to >90%
• Implement a faster version of drugPertubationSignature
• Add additional plotting functions

• Include scripts for differential expression analysis and GSEA of toxico-genomic data (limma)

                    Changes in version 1.0.0                        
  

• Package archived on CRAN
• Package submitted to Biocondcutor
• Modified package to depend on updated CoreGx
• All molecularProfiles are now SummarizedExperiment instead of ExpressionSet

• Abstracted some additional functions to CoreGx

                    Changes in version 0.1.2                        
  

• Updated downloadTSet function to use published Zenodo DOIs to retrieve data

• Modified rankGeneDrugsPerturbation to fix a bad unit conversion which would return concentrations in the wrong unit

                    Changes in version 0.1.1                        
  

• Bug Fix: Regenerated TGGATESsmall (sample dataset) to fix make a result in the vignette consistent with previous releases.

                    Changes in version 0.1.0                        
  

• Rewrote plots using ggplot2 to improve aesthetics
• Also can now extend plotting functions using standard ggplot2 syntax

• Improved package documentation

                    Changes in version 0.0.1                        
  

• Minimal package submitted

TPP

                   Changes in version 3.17.6                        

• fix warnings due to unused argument of select(!!!syms(…)) statement during histogram generation for reference data

                   Changes in version 3.17.5                        
  

• fix bugs and warnings in executable examples

                   Changes in version 3.17.4                        
  

• fix errors in build report on Bioconductor

• fix warnings due to conversion of non-numeric values during 2D-TPP import

• fix warnings in ggplot command

• upgrade deprecated dplyr functions

• make syntax of testthat checks more consistent across files

                  Changes in version 3.17.2-3                       
  

• Fixed bugs and warnings after update to dplyr v1.0.0.

                   Changes in version 3.17.1                        
  

• Fixed bug in tpp2dCreateTPPTRreferenece upon user request (#10)

• removed adding spline fit column from 2DTPP output table

• fixed bug in tpp2dCreateTPPTRReference and made example in vignette work

• removed leftover parameters in tpp2dCreateTPref function

• final fix of tpp2dCreateTPPTRreference and call in vignette now works

                   Changes in version 3.17.0                        
  

• New Bioconductor release candidate

TPP2D

                    Changes in version 1.5.5                        

• new visualization options

• volcanoplot: plot2dTppVolcano

• heatmap of fold changes: plot2dTppFcHeatmap

             Changes in version 1.4.1 (2020-06-20)                  
  

• bug fix in moderated F statistic computation - old version is unneccessarily stringent

trackViewer

                   Changes in version 1.25.4                        

• remove http_status from documentation.

• add function to split the lollipop plot into multiLayers.

                   Changes in version 1.25.3                        
  

• Fix the issue in AddArrowMark that grid changed the unit id.

                   Changes in version 1.25.2                        
  

• Fix the issue if there is interrupt of the internet connection to generate vignette.

                   Changes in version 1.25.1                        
  

• Provide more clearly warning or error message if the input is not sorted or contain NA values.

tradeSeq

             Changes in version 1.3.19 (2020-10-16)                 

• Merged conditions branch into master. Now the master branch can therefore handle multiple conditions. There is a new conditions argument in fitGAM to handle that, and a condition-specific smoother will be fitted for each lineage. There is also a new test, conditionTest, which tests for DE between conditions within a lineage. The way this is done under the hood is exactly like the patternTest.

transite

                    Changes in version 1.6.3                        

• added limits argument for spectrum plot x-values to harmonize color scale of multiple spectrum plots

• replaced Rcpp::RcppArmadillo::sample() with now fixed Rcpp::sample()

                    Changes in version 1.6.2                        
  

• updated paper references

• fixed minor formatting issues

• incremented Roxygen2 version

transomics2cytoscape

                    Changes in version 1.0.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Package introduced.

NEW FEATURES

• Package introduced.

treeio

                   Changes in version 1.13.1                        

• as_tibble for pvclust (2020-06-22, Mon)
• as.phylo and as.treedata methods for pvclust object (2020-06-21, Sun)

TRONCO

                   Changes in version 2.21.1                        

• From Travis-CI to Github Actions

TSCAN

                   Changes in version 1.28.0                        

• Added createClusterMST() to create a cluster-based MST from a variety of inputs, migrated from the scran package.

• Added reportEdges() to report edge coordinates for plotting.

• Added mapCellsToEdges() to map cells to the closest edge on the MST.

• Added orderCells() to compute a pseudotemporal ordering from mapped cells.

• Added quickPseudotime() to wrap MST construction and ordering into a single call.

• Added testPseudotime() to test for DE genes along one or more paths through a MST.

• Added the rowmean() utility to compute column means for row groupings.

• Added perCellEntropy() to compute per-cell entropies across various matrix types.

tximeta

                    Changes in version 1.8.0                        

• Added ‘fromDb’ argument to addIds() to allow IDs to be added from the associated TxDb/EnsDb instead of the org package (which is used by default). Feature suggestion from Kristoffer Vitting-Seerup.

• Added function retrieveCDNA() that will download or load a cached version of the transcript sequences used for quantification. Note that the returned sequences are not ordered or matched to the rows of the SummarizedExperiment object. Feature suggestion from Kristoffer Vitting-Seerup.

• Added function addCDS() that will add CDS ranges for coding transcripts (and fills in original ranges for non-coding), as well as a ‘coding’ column as a logical indicator. Feature suggestion from Kristoffer Vitting-Seerup.

• Added option that environmental variable TXIMETA_HUB_CACHE can be used to set tximeta’s cache location, to avoid prompting the user on the first run of tximeta().

• tximeta() will now pull GENCODE TxDb from AnnotationHub when it is listed there (only Homo sapiens are at this point in time). Thanks to Leonardo Collado-Torres for the suggestion!

• Now summarizeToGene() will add a column tx_ids, which is a CharacterList of the transcript IDs.

                   Changes in version 1.7.13                        
  

• Added ‘fromDb’ argument to addIds() to allow IDs to be added from the associated TxDb/EnsDb instead of the org package (which is used by default). Feature suggestion from Kristoffer Vitting-Seerup.

                   Changes in version 1.7.12                        
  

• Added function retrieveCDNA() that will download or load a cached version of the transcript sequences used for quantification. Note that the returned sequences are not ordered or matched to the rows of the SummarizedExperiment object. Feature suggestion from Kristoffer Vitting-Seerup.

                   Changes in version 1.7.11                        
  

• Added function addCDS() that will add CDS ranges for coding transcripts (and fills in original ranges for non-coding), as well as a ‘coding’ column as a logical indicator. Feature suggestion from Kristoffer Vitting-Seerup.

                   Changes in version 1.7.10                        
  

• Added option that environmental variable TXIMETA_HUB_CACHE can be used to set tximeta’s cache location, to avoid prompting the user on the first run of tximeta().

                    Changes in version 1.7.9                        
  

• tximeta() will now pull GENCODE TxDb from AnnotationHub when it is listed there (only Homo sapiens are at this point in time). Thanks to Leonardo Collado-Torres for the suggestion!

                    Changes in version 1.7.6                        
  

• Now summarizeToGene() will add a column tx_ids, which is a CharacterList of the transcript IDs.

                    Changes in version 1.7.1                        
  

• Updated to Ensembl release 100, GENCODE 34/M25.

tximport

                   Changes in version 1.18.0                        

• Code cleanup for deprecated functions. tximport reads in only alevin version 0.14.0 or greater. For older data, use previous versions of tximport.

UMI4Cats

                   Changes in version 0.99.21                       

• Improvements in vignette and documentation.

                   Changes in version 0.99.20                       
  

• Avoid duplication of fragment end calculation in plotDifferential for DESeq2 results.

                   Changes in version 0.99.19                       
  

• Minor documentation changes to pass Bioconductor checks.

                   Changes in version 0.99.18                       
  

• Fix DESeq2 example.

• Reduce size of installed example tsv.gz count files.

                   Changes in version 0.99.17                       
  

• Re-run example datasets and use again links from figshare.

                   Changes in version 0.99.16                       
  

IMPORTANT

• This version is not compatible with the .tsv.gz files created by previous versions. You will need to run contactsUMI4C() again to generate updated .tsv.gz files.

UPDATES

• Improved grouping arguments for UMI-4C objects: now creates a new UMI-4C object that can be accessed using groupsUMI4C(umi4c)$condition. This allows retaining replicate information in the main UMI4C object while allowing plotting grouped trends stored in groupsUMI4C().

• Added new statistical test using DESeq2: differentialNbinomWaldTestUMI4C().

                   Changes in version 0.99.15                       
  

• Fixed duplicated read number in read id (.singlePrepUMI4C) (see issue #5).

• Changed example download urls to gattaca server.

                   Changes in version 0.99.14                       
  

• Fixed bug where adaptive smoothed trend was normalized twice (see issue #4).

                   Changes in version 0.99.11                       
  

• Uploaded example datasets urls in downloadUMI4CexampleData() to a more stable and permanent location (figshare.com).

                   Changes in version 0.99.10                       
  

• Avoid running long and redundant examples, already tested in the vignette to avoid TIMEOUT build error.

                   Changes in version 0.99.9                        
  

• Add data object ex_ciita_umi4c to use in examples and reduce check running times.

                   Changes in version 0.99.8                        
  

• Update package vignette to clarify the origin of the different sample files used to exemplify a workflow using the UMI4Cats package.

                   Changes in version 0.99.7                        
  

• Added unit tests using testthat.

• Use BiocFileCache to download sample files.

• Use tempdir() for demo purposes both in vignette and examples.

• Added inst\scripts to describe how the sample data was generated.

• Other minor changes to comply with Bioconductor review (see https://github.com/Pasquali-lab/UMI4Cats/issues/2#issue-637249954)

                   Changes in version 0.99.6                        
  

• Delete downloaded and intermediate folders when building vignette.

• Added UMI4Cats_index to .Rbuildignore to prevent ERRORs and WARNINGs in BioCCheck.

                   Changes in version 0.99.5                        
  

• Increased speed of getViewpointCoordinates() by allowing pre-selection of viewpoint chromosome using sel_seqname argument.

• Added reduced fastq files in extdata and allow downloading of reduced bowtie index to increase vignette building speed.

                   Changes in version 0.99.4                        
  

• Added .Rproj files to .gitignore

                   Changes in version 0.99.3                        
  

• Changed example in vignette and manuals to CIITA.

• Added viewpoint name in plotTrend().

• Improved multi-panel plotting of plotUMI4C().

                   Changes in version 0.99.2                        
  

• Allow ref_umi4c to be used as reference for plotting colors, domainogram and differential analysis (not only for normalization).

• Fixed error when using sampleID as grouping variable in makeUMI4C().

• Fixed bug in results() when fomat=data.frame and ordered=TRUE.

• Improved visualization of differential regions reconverting Inf and -Inf to maximum and minimum (respectively) odd’s ratio values.

• Add more functionality details in the Analyzing UMI-4C data with UMI4Cats vignette.

                   Changes in version 0.99.1                        
  

• Fixed error in function createGeneAnnotation and plotGenes that occurs when there are no genes in the region or a gene has multiple identifiers.

• Fixed duplicated generics definition for SummarizedExperiment objects to avoid error when reloading the package.

• Fixed error when bait_exclusion is set to 0.

• Added possibility to specify the sample to use as reference for normalization (ref_umi4c argument in makeUMI4C).

• Now the grouping variable in makeUMI4C() is used more upstream in the analysis. For using different grouping variables, user must create different UMI4C objects.

• Fixed bug where sometimes bait coordinates in the output tsv file are NA.

• statsUMI4C now also outputs a stats summary table in wk_dir/logs/stats_summary.txt.

• Improve function documentation.

• Improve pkgdown UMI4Cats site.

• Rewrite and improve the Analyzing UMI-4C data with UMI4Cats vignette.

                   Changes in version 0.99.0                        
  

• First public release of UMI4Cats.

• Added a NEWS.md file to track changes to the package.

uncoverappLib

                 Changes in version 0.0.0.9000                      

setup

• added NEWS.md creation

universalmotif

                    Changes in version 1.8.0                        

NEW FEATURES

• scan_sequences()/enrich_motifs() can now be used to scan/enrich for gapped motifs. A new section has been added to the SequenceSearches.Rmd vignette.

• scan_sequences(…, use.gaps), enrich_motifs(…, use.gaps): ignore motif gap information.

• read_meme(), write_meme(): now fully support custom alphabets.

• prob_match(), prob_match_bkg(): calculate the probability of a motif match based on background frequencies of the motif object or provided values, respectively.

• enrich_motifs(), get_matches(), get_scores(), motif_pvalue(), motif_score(), scan_sequences(), score_match(): new allow.nonfinite parameter, allowing for the functions to work even if non-finite values are present in the motif PWM.

• read_matrix(…, comment): allows for comments to be ignored in motif files.

• write_matrix(…, digits): control the number of digits to use for writing motif positions.

• New mask_seqs() utility function: inject hard masks into sequences.

• scan_sequences(…, warn.NA), enrich_motifs(…, warn.NA): new option which can disable warnings from non-standard letters being detected in the input sequences.

• get_bkg(…, window, window.size, window.overlap): new options for calculating sequence background in windows.

• get_bkg(…, merge.res): new option to return background information for individual sequences.

• scan_sequences(…, calc.pvals): new option to calculate P-values for sequence hits. This is merely automating using the results from scan_sequences() to calculate P-values manually with motif_pvalue().

• view_motifs(…, show.positions, show.positions.once, show.names): new options for customizing the look of plotted motifs.

MINOR CHANGES

• read_matrix(…, positions): added partial argument matching.

• create_sequences(), shuffle_sequences(), motif_pvalue(): the c++ random engine has been changed from std::default_random_engine to std::mt19937. This should allow for the same rng.seed value to result in the same output regardless of OS.

• score_match() has been vectorized (alongside new prob_match() function).

• The ape and ggtree packages are now no longer imported and must be installed seperately in order to use motif_tree().

• The processx package is no longer imported and must be installed seperately in order to use run_meme().

• The pseudocount slot is now shown when universalmotif class objects are printed.

• get_bkg(): the list.out and as.prob options have been disabled. To simplify the function, the only possible output (exception: if to.meme is not NULL) is a DataFrame showing both counts and probabilities.

• Changed the default look of motifs plotted by view_motifs().

• General documentation cleanup.

BUG FIXES

• Changing motif backgrounds with [<- will now make sure to set correct vector names.

• get_bkg() will now correctly ignore non-standard letters and letters missing from the provided alphabet during counting.

                    Changes in version 1.6.4                        
  

BUG FIXES

• cbind(): do not ignore the pseudocount slot.

• Fixed typo in IntroductionToSequenceMotifs.Rmd.

• Fixed U() function in IntroductionToSequenceMotifs.Rmd, no longer returns NA values if 0s are present.

• read_cisbp(): no parsing errors for motifs with missing/partial header info.

                    Changes in version 1.6.3                        
  

BUG FIXES

• scan_sequences(): commented out WIP code for scanning gapped motifs.

                    Changes in version 1.6.2                        
  

BUG FIXES

• motif_tree(): ‘daylight’ layout is no longer disabled.

                    Changes in version 1.6.1                        
  

BUG FIXES

• summarise_motif(): properly retrieves altname slot. Contribution from Spencer Nystrom (https://github.com/bjmt/universalmotif/pull/9).

• read_meme(): for LIKE type alphabets, make sure PROTEIN-LIKE is understood as being AA.

variancePartition

                   Changes in version 1.19.20                       

• fix bug discovered when the number of features is less than the number of chunks in iterBatch()

                   Changes in version 1.19.19                       
  

• simple bug fixes to pass R CMD check

                   Changes in version 1.19.18                       
  

• simplify calcVarPart for lm and lmer. Add compatibility for glm

• Simplify checkModelStatus.merMod to allow formula (A|B) where A is continuous

• remove unused “adjust” arguments for clarity

                   Changes in version 1.19.17                       
  

• add get_prediction() for results of lm()

• improve documentation of get_prediction()

                   Changes in version 1.19.16                       
  

• in canCorPairs() change statistic used to summarize CCA to Cramer’s V. The difference is very subtle, but is now based on first principles.

• in dream, check that data is a data.frame

• dream() defaults to computeResiduals=TRUE for compatability with zenith

                   Changes in version 1.19.14                       
  

• fix issue with residuals() where examples fail

                   Changes in version 1.19.13                       
  

• fix issues with residuals()
  • https://github.com/GabrielHoffman/variancePartition/issues/18

• fix issue exporting eBayes, topTable, etc

                   Changes in version 1.19.12                       
  

• Improve documentation for contrasts in dream.Rmd

• check that contrasts sum to zero in plotContrasts.

                   Changes in version 1.19.11                       
  

• in voomWithDreamWeights() fix issue with not defining design

  • https://github.com/GabrielHoffman/variancePartition/issues/17

                   Changes in version 1.19.10                       
    

• in voomWithDreamWeights() fix issue with returning design matrix

• better error if counts can’t be converted to matrix

  • https://github.com/GabrielHoffman/variancePartition/issues/15

                   Changes in version 1.19.7                        
    

• Round numbers in plotContrasts()

• fix issues with strings are passed to formula arguments

                   Changes in version 1.19.6                        
  

• New gives meaning full error message for dream(), etc when variable is not found in data.

                   Changes in version 1.19.5                        
  

• Better error catching when running fitVarPartModel() with fxn that fails

• add get_prediction() function

  • the following code now can be run in parallel fitList = fitVarPartModel( Y, ~ (1|Batch), data, fxn = function(fit){ B = variancePartition::get_prediction(fit, ~(1|Batch)) fit@resp$y - B }, BPPARAM=SnowParam(3))

                   Changes in version 1.19.4                        
    

• Update vignette #3, and update documentation of REML argument

                   Changes in version 1.19.3                        
  

• add new FAQ.Rmd

                   Changes in version 1.19.2                        
  

• canCorPairs() now returns NA correlation when two variables have no overlapping observed values

• plotCorrMatrix() now handles NA correlation values

                   Changes in version 1.19.1                        
  

• Bump to next Bioconductor version

                   Changes in version 1.18.3                        
  

• Improve documentation

• move location of eBayesFMT code

                   Changes in version 1.18.2                        
  

• Clean up some code and add documentation

• document ebayesFMT

                   Changes in version 1.18.1                        
  

• Clean up some code and add documentation

• compute effective degrees of freedom for each model

VariantAnnotation

                   Changes in version 1.36.0                        

NEW FEATURES

• ref<-, alt<-, qual<- and filt<- allow replacement value length recycling

velociraptor

                   Changes in version 0.99.9                        

• Converted various functions to S4 generics for easier use with SingleCellExperiment objects.

                   Changes in version 0.99.8                        
  

• Trigger new build to repeat ExperimentHub download.

                   Changes in version 0.99.7                        
  

• Delete empty line to force cache update. See https://github.com/rubocop-hq/rubocop/pull/4342#issuecomment-305449759.

                   Changes in version 0.99.6                        
  

• Set autoscale=FALSE in the call to scvelo function velocity_embedding to avoid issue related to Qt and plotting.

                   Changes in version 0.99.5                        
  

• Trigger new build to check if Windows issue resolved itself.

                   Changes in version 0.99.4                        
  

• Trigger new build to check whether TIMEOUT issue on Windows is reproducible.

                   Changes in version 0.99.3                        
  

• Explicitly declare all Conda dependencies for scvelo.

                   Changes in version 0.99.2                        
  

• Add hexsticker.

                   Changes in version 0.99.1                        
  

• Remove .Rproj file from git repository.

                   Changes in version 0.99.0                        
  

• First submission to Bioconductor.

VERSO

                    Changes in version 1.0.0                        

• Package released in October 2020.

ViSEAGO

                     Changes in version 1.3                         

• print graph with orca

• Ensembl2GO() biomart update

• show_heatmap() upgrade

• upset print update

• merge_enrich_terms upgrade pvalue cutoff

• merge_enrich_terms globale upgrade

• GOterms_heatmap remove row side colors text and correct showIC column

• vignettes update

• annotate() update for uniprot

• fgsea support

VplotR

             Changes in version 0.5.0 (2020-05-25)                  

• IMPORTANT:

• Created plotProfile function

• MINOR:

• Changed color scale to scico package, roma scale

             Changes in version 0.4.2 (2020-05-10)                  
  

• IMPORTANT:

• Improved nucleosomeEnrichment and background computation
• Treat strands separately in computeVmat

• Added plot theming

• MINOR:

• Clarified normalization approaches
• Improved documentation
• Make computeVmat a bit faster by removing some intermediate steps

wavClusteR

                   Changes in version 2.23.0                        

• Deprecated CWT-based cluster boundary identification

weitrix

                   Changes in version 1.1.10                        

• Fix bug with weitrix_confects due to [[ ]] <- NULL deleting elements from a list instead of storing NULL in the list.

                    Changes in version 1.1.9                        
  

• Peaks were sometimes in reverse order in APA example, data file updated.

• Try to get rid of an odd new build error about stack usage by using serial processing in vignettes.

                    Changes in version 1.1.8                        
  

• Use geom_bin2d in weitrix_calplot scatterplots.

                    Changes in version 1.1.7                        
  

• Add mu_min, mu_max arguments to weitrix_calibrate_all.

                    Changes in version 1.1.6                        
  

• Use glm2, which is less prone to optimization failure.
• Auto-disable parallel processing if X11 device is open.

• Add SLAM-Seq vignette.

                    Changes in version 1.1.5                        
  

• well_knotted_spline for natural splines with good choice of knots.

                    Changes in version 1.1.4                        
  

• weitrix_confects for differential testing.
• weitrix_rms_confects now called weitrix_sd_confects.

• weitrix_calplot now shows mean trend and mean +/- standard deviation trend.

                    Changes in version 1.1.3                        
  

• weitrix_calibrate_all now includes a simple scaling factor to account for residuals from a fitted model being smaller than residuals from the true model.
• weitrix_calplot blue guidelines are similarly adjusted.

• Add weitrix_rms_confects to find rows with confidently excessive variation.

                    Changes in version 1.1.2                        
  

• Vignettes use weitrix_calibrate_all, demonstrate weitrix_calplot.

• weitrix_calplot now uses sqrt(weight)*residual on y axis.

                    Changes in version 1.1.1                        
  

• Switch calibration from linear model on log dispersions to using a gamma GLM.
• Add weitrix_calibrate_all function for very flexible calibration.
• Add weitrix_calplot to examine quality of weights.

wpm

                   Changes in version 0.99.13                       

• Added a zzz.R file for the welcome message when loading the package in an R session
• Corrections in package vignette and Help tab of the shiny app

• Revised all documentation of functions

                   Changes in version 0.99.12                       
  

• fixed the lack of display of images in the help tab
• fixed inconsistencies regarding the setting of quotes when importing data

• added an infobox for plate dimensions compatibility with the number of samples

                   Changes in version 0.99.11                       
  

• fixed issue #10
• fixed issue #22
• changed the display of the datatable in the Results tab

• updated Vignette and Help page about toy dataset (CSV section)

                   Changes in version 0.99.10                       
  

• corrected unit tests for CSV import
• corrected README R commands for convertCSV section
• corrected Help tab for the upload file section

• corrected the Parameters section in the Vignette

             Changes in version 0.99.9 (2020-06-18)                 
  

• Resolved crashes regarding bad settings when importing CSV
• Parameter sections are now collapsible
• created module for number of iterations
• defined the launch for the browser on port 8000
• changed the order of CSV import section in the parameters Panel
• some upload parameters are now available only if the CSV file is correctly imported

• added preview of CSV file when importing in the UI

             Changes in version 0.99.8 (2020-06-11)                 
  

• Modified structure of the Home tab in the shiny application
• Added new module for the help tab.
• Created the help.md file for the Help tab of the app.
• Added CSS for tables, and images.
• Changed the “blank” word to “buffer” throughout the package.
• Changed the “not random” term to “fixed” throughout the package.

• Updated images and text in the tutorial vignette.

             Changes in version 0.99.7 (2020-06-05)                 
  

• Added the convertSE function to manage SummarizedExperiments objects in command line version
• Added the grouping factor option for data import (managed for both shiny app and command line). Now the user can specify the column name corresponding to the grouping factor wpm has to use for backtracking.
• Modified app_ui structure regarding the project title input
• Updated the tutorial vignette’s content
• Updated README file
• Revised unit tests for import functions
• The WPM package version output in Home panel is now obtained with packageVersion()

• Created a new module for the integration of markdown files in the shiny application.

             Changes in version 0.99.6 (2020-06-02)                 
  

• Added function checkWpmInputs to control the correct use of the wrapperWpm function (command line use).

• Updated the README file and the tutorial vignette explaining how to use WPM using command line.

             Changes in version 0.99.5 (2020-06-02)                 
  

• Added functions for importing CSV files and ExpressionSet / MSnSet objects
• Added the wrapper function allowing to use wpm in command line
• Added support for eSet and MSnSet objects as input of the wrapper function

• Added unit tests for import functions

             Changes in version 0.99.4 (2020-05-28)                 
  

• Fix the TIMEOUT error during R CMD CHECK

             Changes in version 0.99.3 (2020-05-28)                 
  

• All the R code is now in the /R directory.
• Modified R code structure by creating additional modules:
• mod_home, fusion between the Home panel and the Help Panel
• mod_data_export, a specific module for data export
• mod_plate_dimensions
• mod_special_wells, mainly to avoid code redundancy and gain readability
• Added unit test for the convertVector2Df function

• Added Rd examples for convertVector2Df and drawMap functions

                   Changes in version 0.99.2                        
  

• Added a NEWS.md file to track changes to the package
• Modified code and files structure of the package
• Added Roxygen comments to functions

xcms

                   Changes in version 3.11.8                        

• Disable parallel processing in vignettes.

                   Changes in version 3.11.7                        
  

• More efficient splitting data per file especially for larger data sets.

• Disable parallel processing in examples.

                   Changes in version 3.11.6                        
  

• Add FilterIntensityParam to filter chromatographic peaks on intensity (issue #502).

• Add estimatePrecursorIntensity function to determine the precursor intensity for MS2 spectra from the neighboring MS1 spectra.

                   Changes in version 3.11.4                        
  

• Change from Spectra and Chromatograms to MSpectra and MChromatograms from MSnbase version >= 2.15.3.

                   Changes in version 3.11.3                        
  

• reconstructChromPeakSpectra: report also polarity and precusorIntensity.

• reconstructChromPeakSpectra: ensure a retention time is reported for reconstructed MS2 spectra (issue #485).

• Change default for expandRt to 0 in reconstructChromPeakSpectra.

• Fix error in refineChromPeaks,MergeNeighboringPeaksParam if no peaks found to be merged.

                   Changes in version 3.11.2                        
  

• Add fillChromPeaks,ChromPeakAreaParam to base the area from which missing peak data should be filled-in on the actually detected chromatographic peaks of a feature.

• Potential fix for issue #481: function should no longer throw an error because retention times are of length 0.

• More efficient splitting of processing which should increase the speed of the findChromPeaks, refineChromPeaks, reconstructChromPeakSpectra and chromPeakSpectra calls.

                   Changes in version 3.11.1                        
  

• Fix issue #471: conversion from XCMSnExp to xcmsSet looses phenodata (thanks to Andris Jankevics for reporting and providing a solution).

• Add normalize method for Chromatogram and Chromatograms objects.

• featureChromatograms gets new parameter n and value to extract EICs only from the top n samples with highest intensities.

• filterFile gets new parameter keepFeatures to support retaining correspondence results even if a data set is filtered by file.

• Export the virtual Param class.

• Add filterColumnsIntensityAbove method for Chromatograms object that allows to select columns (samples) of an Chromatograms object for which intensities of its chromatographic data are higher than a threshold.

• Add removeIntensity method for Chromatogram, Chromatograms, XChromatogram and XChromatograms objects allowing to remove intensities based on different criteria.

• Add correlate method for Chromatograms allowing to correlate multiple chromatograms with each other.

zellkonverter

                    Changes in version 1.0.0                        

• Accepted into Bioconductor for Release 3.12

• zellkonverter provides methods to convert between Python AnnData objects and SingleCellExperiment objects. These are primarily intended for use by downstream Bioconductor packages that wrap Python methods for single-cell data analysis. It also includes functions to read and write H5AD files used for saving AnnData objects to disk.

zinbwave

             Changes in version 1.11.6 (2020-07-18)                 

• Fixed a bug in the initialization of beta_j.

• Fixed a bug in zinbsurf.

• Changed zinbwave default to K=2.

• Fix bug in the initialization of W.

NEWS from new and existing Data Experiment Packages

chipseqDBData

                    Changes in version 1.6.0                        

• Return BamFile objects from all getter functions, to properly capture index files with different names from the BAM files.

clustifyrdatahub

             Changes in version 0.99.4 (2020-09-02)                 

• Add mouse atlas

             Changes in version 0.99.0 (2020-07-02)                 
  

• Cleanup for bioc

curatedTCGAData

                   Changes in version 1.12.0                        

Bug fixes and minor improvements

• Output dataset options as table when dry.run is enabled in the main function.

• Check for RaggedExperiment dependency when loading data that uses the data representation (@vjcitn, #39)

depmap

                     Changes in version 1.3                         

Changes in version 1.3.2

• 20Q3 data added for crispr, copyNumber, TPM, mutationCalls and metadata datasets. Newer versions for the other datasets were not released.

Changes in version 1.3.1

• 20Q2 data added
• Included new proteomic dataset
• expression variable in TPM dataset changed to rna_expression

dorothea

             Changes in version 1.1.2 (2020-10-08)                  

• Changed TF census from TFclass to the more recent version from Lambert et al.. Information of mode of regulation for each TF (activator, supressor, dual) is still taken from Garcia-Alonso et al..

• Updated deprecated gene symbols to their latest version with the limma package (version 3.44.3).

• Shifted viper package from suggest to depends in the DESCRIPTION file.

• Added a further argument specifially for run_viper().Seurat to select a specific assay name to extract the normalized gene expression values from.

             Changes in version 1.1.1 (2020-09-02)                  
  

• Export df2regulon function

• Improved documentation (added gh page URL to DESCRIPTION)

             Changes in version 1.0.1 (2020-08-13)                  
  

• Improved package documentation

• Updated link to 10x genomics data set in single-cell vignette

• Fixed tests related to Seurat and SCE class

dsQTL

                    Changes in version 2.17                         

USER VISIBLE CHANGES

• ch2locs (retrievable via dsQTL::getSNPlocs) has been changed at about 1850 locations where rs numbers had been associated with hg19 addresses; the dsQTL regions are hg18 as are all the chr2… SNP addresses. Previously the discoverable rs numbers used in the Chicago distribution from http://eqtl.uchicago.edu/dsQTL_data/GENOTYPES/ had be mapped via SNPlocs…20111119, but now they come directly from the Chicago text file.

FieldEffectCrc

             Changes in version 0.99.2 (2020-09-20)                 

• (0.99.2) Added PMCID and PMID in reference to original study

• (0.99.2) Updated citation to include full reference

• (0.99.2) Minor improvements in readability of R code

             Changes in version 0.99.1 (2020-07-24)                 
  

• (0.99.1) Simplified vignette Installation code

• (0.99.1) Updated vignette typical-filter code chunk to evaluate as R code

             Changes in version 0.99.0 (2020-07-14)                 
  

• (0.99.0) Passed R CMD check and R CMD BiocCheck without errors or warnings

• (0.99.0) Submitted to Bioconductor

             Changes in version 0.1.0 (2020-07-03)                  
  

• (0.1.0) Begin building FieldEffectCrc package

MethylSeqData

                    Changes in version 1.0.0                        

• New package MethylSeqData, providing DNA methylation sequencing datasets.

pRolocdata

                   Changes in version 1.27.1                        

• add data from Kozik et al. (2020)

RegParallel

                    Changes in version 1.8.0                        

• added funtionality for include survey weights via survey::svyglm

• fixed bug whereby, in ceratin situations, an incorrect number of blocks would be calculated

RforProteomics

                   Changes in version 1.27.1                        

• Remove deprecated IPPD dependency

SCATEData

                    Changes in version 1.0.0                        

• submission to Bioconductor

scRNAseq

                    Changes in version 2.4.0                        

• Added the Zilionis lung dataset (Jens Preussner).

• Added the Hermann spermatogenesis dataset (Charlotte Soneson).

• Added the Mair and Kotliarov PBMC datasets (Stephany Orjuela).

• Added the Stoeckius cell hashing dataset.

• Added the Wu kidney snRNA-seq dataset.

• Added the Hu cortex snRNA-seq dataset.

• Added spike-in concentrations to the altExp rowData for various datasets (Alan O’Callaghan).

signatureSearchData

             Changes in version 1.2.1 (2020-08-14)                  

• Edited vignette containing ‘DEGs and Cutoffs Definition’ subsections to document how to defining query DEGs and gene set reference database by setting LFC scores and FDR cutoffs.

SingleCellMultiModal

                    Changes in version 1.2.0                        

New features

• CITEseq function, vignette, and ‘cord_blood’ data available (@drighelli, #18)

• Include seqFISH function, vignette, and ‘mouse_visual_cortex’ data (v1 and v2 from @drighelli, #14)

• New ‘mouse_gastrulation’ dataset released (version “2.0.0”).

• Use version argument to indicate the mouse_gastrulation data version

• The data includes all cells not only the ones that passed the QC of all three ‘omics (thanks @rargelaguet, @ajabadi).

Bug fixes and minor improvements

• Caching mechanism uses tools::R_user_dir and not rappdirs.

• Improved display of available data using ExperimentHub metadata.

• Improved documentation explaining versioning differences.

• Contribution guidelines available at https://github.com/waldronlab/SingleCellMultiModal/wiki/Contributing-Guidelines

• Default version argument in scNMT function now set to “2.0.0” (version “1.0.0” still available)

spatialLIBD

                    Changes in version 1.1.5                        

NEW FEATURES

• fetch_data() takes the data from sce object and creates a VisiumExperiment object containing these data. VisiumExperiment object can be obtained with fetch_data(“ve”).

                    Changes in version 1.1.4                        
  

NEW FEATURES

• fetch_data() now uses BiocFileCache() when downloading the data from Dropbox.

timecoursedata

             Changes in version 0.99.0 (2020-05-15)                 

• Submitted to Bioconductor

TMExplorer

                   Changes in version 0.99.6                        

• Renamed Vignette to TMExplorer (“tutorial” was too generic)

• More man page updates

                   Changes in version 0.99.5                        
  

• Updated man pages and cleaned up some code.

             Changes in version 0.99.3 (2020-07-03)                 
  

• Fixed a bug when downloading data on Windows

             Changes in version 0.99.2 (2020-07-03)                 
  

• Fixed missing cell type labels in some datasets

             Changes in version 0.99.1 (2020-06-25)                 
  

• Now uses SingleCellExperiment objects

             Changes in version 0.99.0 (2020-06-22)                 
  

• Submitted to Bioconductor

NEWS from new and existing Workflows

fluentGenomics

                    Changes in version 1.0.1                        

• fix downloading of ATAC seq files for windows

Deprecated and Defunct Packages

Fifty Six software packages were removed from this release (after being deprecated in Bioc 3.11): affypdnn, AnalysisPageServer, anamiR, BayesPeak, bgafun, biosvd, birta, CALIB, CAMTHC, cellGrowth, chroGPS, cobindR, CTDquerier, CVE, DChIPRep, DEDS, DupChecker, FEM, gCMAP, gCMAPWeb, geecc, Genominator, IdMappingAnalysis, IdMappingRetrieval, IPPD, kimod, LMGene, lol, LVSmiRNA, M3D, manta, MaxContrastProjection, MCRestimate, MergeMaid, mitoODE, MoPS, motifRG, MTseeker, nem, PAPi, pcaGoPromoter, pint, plw, PowerExplorer, proteoQC, QUALIFIER, readat, RefNet, RIPSeeker, SANTA, scfind, splicegear, sRAP, triform, Vega, waveTiling

Sixty eight software are deprecated in this release and will be removed in Bioc 3.13: adaptest, ArrayTV, BioSeqClass, CGEN, CHARGE, chimera, CNVtools, CorMut, DESeq, explorase, flowFit, flowSpy, flowType, flowVS, focalCall, FourCSeq, FunciSNP, GeneticsDesign, GenRank, GGBase, GGtools, GOFunction, gQTLBase, gQTLstats, hicrep, ImpulseDE, ImpulseDE2, joda, JunctionSeq, LINC, Logolas, mcaGUI, metaArray, metaseqR, methVisual, methyvim, Mirsynergy, MmPalateMiRNA, MOFA (Please see MOFA2), MotIV, NarrowPeaks, netbenchmark, netReg, OGSA, OmicsMarkeR, pathprint, PathwaySplice, PGA, PGSEA, plrs, prada, Prize, Rariant, reb, Roleswitch, rTANDEM, sampleClassifier, sapFinder, scsR, shinyTANDEM, sigaR, signet, simpleaffy, spotSegmentation, Starr, SVAPLSseq, TxRegInfra, xps

Two experimental data packages were removed this release (after being deprecated in BioC 3.11): MTseekerData, RIPSeekerData

Sixteen experimental data packages are deprecated in this release and will be removed in Bioc 3.13: flowFitExampleData, FunciSNP.data, geuvPack, geuvStore2, GGdata, methyvimData, mitoODEdata, Mulder2012, pathprintGEOData, pcaGoPromoter.Hs.hg19, pcaGoPromoter.Mm.mm9, pcaGoPromoter.Rn.rn4, RNAinteractMAPK, sampleClassifierData, waveTilingData, yriMulti

Nine annotation packages were supposed to be removed this release, however we decided to give an extra cycle for maintainers to adapt and will be removed in 3.13: hom.At.inp.db, hom.Ce.inp.db, hom.Dm.inp.db, hom.Dr.inp.db, hom.Hs.inp.db, hom.Mm.inp.db, hom.Rn.inp.db, hom.Sc.inp.db, KEGG.db.

Five annotation packages are deprecated in this release and will be removed in Bioc 3.13: MeSH.Eco.55989.eg.db, MeSH.Eco.ED1a.eg.db, MeSH.Eco.IAI39.eg.db, MeSH.Eco.UMN026.eg.db, MeSH.Eqc.eg.db (renamed to MeSH.Eca.eg.db)

No workflow packages were removed in this release.

No workflow packages were deprecated in this release.