May 3, 2019

Bioconductors:

We are pleased to announce Bioconductor 3.9, consisting of 1741 software packages, 371 experiment data packages, 948 annotation packages, and 27 workflows.

There are 105 new software packages, 13 new data experiment packages, 4 new workflows, and many updates and improvements to existing packages; Bioconductor 3.9 is compatible with R 3.6.0, and is supported on Linux, 32- and 64-bit Windows, and Mac OS X. This release will include an updated Bioconductor Amazon Machine Image and Docker containers.

Visit https://bioconductor.org for details and downloads.

Contents

• Getting Started with Bioconductor 3.9
• New Software Packages
• New Data Experiment Packages
• New Workflows
• 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 3.9

To update to or install Bioconductor 3.9:

1. Install R >=3.6.0. Bioconductor 3.9 has been designed expressly for this version of R.

2. Follow the instructions at http://bioconductor.org/install/.

New Software Packages

There are 105 new software packages in this release of Bioconductor.

• ADAM ADAM is a GSEA R package created to group a set of genes from comparative samples (control versus experiment) belonging to different species according to their respective functions (Gene Ontology and KEGG pathways as default) and show their significance by calculating p-values referring togene diversity and activity. Each group of genes is called GFAG (Group of Functionally Associated Genes).

• ADAMgui ADAMgui is a Graphical User Interface for the ADAM package. The ADAMgui package provides 2 shiny-based applications that allows the user to study the output of the ADAM package files through different plots. It’s possible, for example, to choose a specific GFAG and observe the gene expression behavior with the plots created with the GFAGtargetUi function. Features such as differential expression and foldchange can be easily seen with aid of the plots made with GFAGpathUi function.

• adductomicsR Processes MS2 data to identify potentially adducted peptides from spectra that has been corrected for mass drift and retention time drift and quantifies MS1 level mass spectral peaks.

• alevinQC Generate QC reports summarizing the output from an alevin run. Reports can be generated as html or pdf files, or as shiny applications.

• AMARETTO Integrating an increasing number of available multi-omics cancer data remains one of the main challenges to improve our understanding of cancer. One of the main challenges is using multi-omics data for identifying novel cancer driver genes. We have developed an algorithm, called AMARETTO, that integrates copy number, DNA methylation and gene expression data to identify a set of driver genes by analyzing cancer samples and connects them to clusters of co-expressed genes, which we define as modules. We applied AMARETTO in a pancancer setting to identify cancer driver genes and their modules on multiple cancer sites. AMARETTO captures modules enriched in angiogenesis, cell cycle and EMT, and modules that accurately predict survival and molecular subtypes. This allows AMARETTO to identify novel cancer driver genes directing canonical cancer pathways.

• animalcules animalcules is an R package for utilizing up-to-date data analytics, visualization methods, and machine learning models to provide users an easy-to-use interactive microbiome analysis framework. It can be used as a standalone software package or users can explore their data with the accompanying interactive R Shiny application. Traditional microbiome analysis such as alpha/beta diversity and differential abundance analysis are enhanced, while new methods like biomarker identification are introduced by animalcules. Powerful interactive and dynamic figures generated by animalcules enable users to understand their data better and discover new insights.

• atSNP atSNP performs affinity tests of motif matches with the SNP or the reference genomes and SNP-led changes in motif matches.

• BANDITS BANDITS is a Bayesian hierarchical model for detecting differential splicing of genes and transcripts, via differential transcript usage (DTU), between two or more conditions. The method uses a Bayesian hierarchical framework, which allows for sample specific proportions in a Dirichlet-Multinomial model, and samples the allocation of fragments to the transcripts. Parameters are inferred via Markov chain Monte Carlo (MCMC) techniques and a DTU test is performed via a multivariate Wald test on the posterior densities for the average relative abundance of transcripts.

• batchelor Implements a variety of methods for batch correction of single-cell (RNA sequencing) data. This includes methods based on detecting mutually nearest neighbors as well as a simple sparsity-preserving translation of the population means. Functions are also provided for global rescaling to remove differences in depth between batches, and to perform a principal components analysis that is robust to differences in the numbers of cells across different batches.

• bigPint Methods for visualizing large multivariate datasets using static and interactive scatterplot matrices, parallel coordinate plots, volcano plots, and litre plots. Includes examples for visualizing RNA-sequencing datasets and differentially expressed genes.

• BiocSingular Implements exact and approximate methods for singular value decomposition and principal components analysis, in a framework that allows them to be easily switched within Bioconductor packages or workflows. Where possible, parallelization is achieved using the BiocParallel framework.

• BioMM The identification of reproducible biological patterns from high-dimensional omics data is a key factor in understanding the biology of complex disease or traits. Incorporating prior biological knowledge into machine learning is an important step in advancing such research. We have proposed a biologically informed multi-stage machine learing framework termed BioMM specifically for phenotype prediction based on omics-scale data where we can evaluate different machine learning models with various prior biological meta information.

• celda celda leverages Bayesian hierarchical modeling to cluster genes, cells, or both simultaneously from single cell sequencing data.

• CellBench This package contains infrastructure for benchmarking analysis methods and access to single cell mixture benchmarking data. It provides a framework for organising analysis methods and testing combinations of methods in a pipeline without explicitly laying out each combination. It also provides utilities for sampling and filtering SingleCellExperiment objects, constructing lists of functions with varying parameters, and multithreaded evaluation of analysis methods.

• CellMixS Evaluate Cellspecific Mixing Scores (CMS) for different batches/groups in scRNA-seq data.

• CHETAH CHETAH is a accurate, selective and fast scRNA-seq classifier. Classification is guided by a reference dataset, preferentially also a scRNA-seq dataset. By hierarchical clustering of the reference data, CHETAH creates a classification tree that enables a step-wise, top-to-bottom classification. Using a novel stopping rule, CHETAH classifies the input cells to the cell types of the references and to “intermediate types”: more general classifications that ended in an intermediate node of the tree.

• CluMSID CluMSID is a tool that aids the identification of features in untargeted LC-MS/MS analysis by the use of MS2 spectra similarity and unsupervised statistical methods. It offers functions for a complete and customisable workflow from raw data to visualisations and is interfaceable with the xmcs family of preprocessing packages.

• CNVRanger The CNVRanger package implements a comprehensive tool suite for CNV analysis. This includes functionality for summarizing individual CNV calls across a population, assessing overlap with functional genomic regions, and association analysis with gene expression and quantitative phenotypes.

• cola Subgroup classification is a basic task in genomic data analysis, especially for gene expression data and methylation data. It can predict novel subgroups when there is nothing known about the data or it can test consistency between predicted subgroups with known annotations. The cola package provides a general framework for subgroup classification by consensus clustering. It has following features: 1. It modularizes the consensus clustering processes that various methods can be easily integrated. 2. It provides rich visualizations for interpreting the results. 3. It allows running multiple methods at the same time and provides functionalities to compare results in a straightforward way. 4. It provides a new method to extract features which are more efficient to separate subgroups. 5. It allows doing partitioning in a hierarchical way to detect subgroups with relatively smaller difference. 6. It generates detailed reports for the complete analysis.

• CopyNumberPlots CopyNumberPlots have a set of functions extending karyoploteRs functionality to create beautiful, customizable and flexible plots of copy-number related data.

• CoRegFlux CoRegFlux aims at providing tools to integrate reverse engineered gene regulatory networks and gene-expression into metabolic models to improve prediction of phenotypes, both for metabolic engineering, through transcription factor or gene (TF) knock-out or overexpression in various conditions as well as to improve our understanding of the interactions and cell inner-working.

• cytofast Multi-parametric flow and mass cytometry allows exceptional high-resolution exploration of the cellular composition of the immune system. Together with tools like FlowSOM and Cytosplore it is possible to identify novel cell types. By introducing cytofast we hope to offer a workflow for visualization and quantification of cell clusters for an efficient discovery of cell populations associated with diseases or other clinical outcomes.

• dcanr Methods and an evaluation framework for the inference of differential co-expression/association networks.

• deco This package discovers differential features in hetero- and homogeneous omic data by a two-step method including subsampling LIMMA and NSCA. DECO reveals feature associations to hidden subclasses not exclusively related to higher deregulation levels.

• decompTumor2Sig Uses quadratic programming for signature refitting, i.e., to decompose the mutation catalog from an individual tumor sample into a set of given mutational signatures (either Alexandrov-model signatures or Shiraishi-model signatures), computing weights that reflect the contributions of the signatures to the mutation load of the tumor.

• DelayedDataFrame Based on the standard DataFrame metaphor, we are trying to implement the feature of delayed operation on the DelayedDataFrame, with a slot of lazyIndex, which saves the mapping indexes for each column of DelayedDataFrame. Methods like show, validity check, [/[[ subsetting, rbind/cbind are implemented for DelayedDataFrame to be operated around lazyIndex. The listData slot stays untouched until a realization call e.g., DataFrame constructor OR as.list() is invoked.

• DeMixT DeMixT is a software package that performs deconvolution on transcriptome data from a mixture of two or three components.

• DepecheR The purpose of this package is to identify traits in a dataset that can separate groups. This is done on two levels. First, clustering is performed, using an implementation of sparse K-means. Secondly, the generated clusters are used to predict outcomes of groups of individuals based on their distribution of observations in the different clusters. As certain clusters with separating information will be identified, and these clusters are defined by a sparse number of variables, this method can reduce the complexity of data, to only emphasize the data that actually matters.

• DiscoRhythm Set of functions for estimation of cyclical characteristics, such as period, phase, amplitude, and statistical significance in large temporal datasets. Supporting functions are available for quality control, dimensionality reduction, spectral analysis, and analysis of experimental replicates. Contains a R Shiny web interface to execute all workflow steps.

• divergence This package provides functionality for performing divergence analysis as presented in Dinalankara et al, “Digitizing omics profiles by divergence from a baseline”, PANS 2018. This allows the user to simplify high dimensional omics data into a binary or ternary format which encapsulates how the data is divergent from a specified baseline group with the same univariate or multivariate features.

• DNABarcodeCompatibility The package allows one to obtain optimized combinations of DNA barcodes to be used for multiplex sequencing. In each barcode combination, barcodes are pooled with respect to Illumina chemistry constraints. Combinations can be filtered to keep those that are robust against substitution and insertion/deletion errors thereby facilitating the demultiplexing step. In addition, the package provides an optimizer function to further favor the selection of barcode combinations with least redundancy of DNA barcodes.

• doseR doseR package is a next generation sequencing package for sex chromosome dosage compensation which can be applied broadly to detect shifts in gene expression among an arbitrary number of pre-defined groups of loci. doseR is a differential gene expression package for count data, that detects directional shifts in expression for multiple, specific subsets of genes, broad utility in systems biology research. doseR has been prepared to manage the nature of the data and the desired set of inferences. doseR uses S4 classes to store count data from sequencing experiment. It contains functions to normalize and filter count data, as well as to plot and calculate statistics of count data. It contains a framework for linear modeling of count data. The package has been tested using real and simulated data.

• enrichTF As transcription factors (TFs) play a crucial role in regulating the transcription process through binding on the genome alone or in a combinatorial manner, TF enrichment analysis is an efficient and important procedure to locate the candidate functional TFs from a set of experimentally defined regulatory regions. While it is commonly accepted that structurally related TFs may have similar binding preference to sequences (i.e. motifs) and one TF may have multiple motifs, TF enrichment analysis is much more challenging than motif enrichment analysis. Here we present a R package for TF enrichment analysis which combine motif enrichment with the PECA model.

• epihet epihet is an R-package that calculates the epigenetic heterogeneity between cancer cells and/or normal cells. The functions establish a pipeline that take in bisulfite sequencing data from multiple samples and use the data to track similarities and differences in epipolymorphism,proportion of discordantly methylated sequencing reads (PDR),and Shannon entropy values at epialleles that are shared between the samples.epihet can be used to perform analysis on the data by creating pheatmaps, box plots, PCA plots, and t-SNE plots. MA plots can also be created by calculating the differential heterogeneity of the samples. And we construct co-epihet network and perform network analysis.

• evaluomeR Evaluating the reliability of your own metrics and the measurements done on your own datasets by analysing the stability and goodness of the classifications of such metrics.

• fishpond Fishpond contains methods for differential transcript and gene expression analysis of RNA-seq data using inferential replicates for uncertainty of abundance quantification, as generated by Gibbs sampling or bootstrap sampling.

• GAPGOM Collection of various measures and tools for lncRNA annotation prediction put inside a redistributable R package. The package contains two main algorithms; lncRNA2GOA and TopoICSim. lncRNA2GOA tries to annotate novel genes (in this specific case lncRNAs) by using various correlation/geometric scoring methods on correlated expression data. After correlating/scoring, the results are annotated and enriched. TopoICSim is a topologically based method, that compares gene similarity based on the topology of the GO DAG by information content (IC) between GO terms.

• GladiaTOX GladiaTOX R package is an open-source, flexible solution to high-content screening data processing and reporting in biomedical research. GladiaTOX takes advantage of the tcpl core functionalities and provides a number of extensions: it provides a web-service solution to fetch raw data; it computes severity scores and exports ToxPi formatted files; furthermore it contains a suite of functionalities to generate pdf reports for quality control and data processing.

• GNET2 Cluster genes to functional groups with E-M process. Iteratively perform TF assigning and Gene assigning, until the assignment of genes did not change, or max number of iterations is reached.

• gpuMagic The package aims to help users write openCL code with little or no effort. It is able to compile an user-defined R function and run it on a device such as a CPU or a GPU. The user can also write and run their openCL code directly by calling .kernel function.

• graper This package enables regression and classification on high-dimensional data with different relative strengths of penalization for different feature groups, such as different assays or omic types. The optimal relative strengths are chosen adaptively. Optimisation is performed using a variational Bayes approach.

• HCABrowser Search, browse, reference, and download resources from the Human Cell Atlas data portal. Development of this package is supported through funds from the Chan / Zuckerberg initiative.

• HumanTranscriptomeCompendium Provide tools for working with a compendium of human transcriptome sequences (originally htxcomp).

• hypeR Geneset enrichment analysis based on hyper-geometric test.

• infercnv Using single-cell RNA-Seq expression to visualize CNV in cells.

• IsoCorrectoRGUI IsoCorrectoRGUI is a Graphical User Interface for the IsoCorrectoR package. IsoCorrectoR performs the correction of mass spectrometry data from stable isotope labeling/tracing metabolomics experiments with regard to natural isotope abundance and tracer impurity. Data from both MS and MS/MS measurements can be corrected (with any tracer isotope: 13C, 15N, 18O…), as well as high resolution MS data from multiple-tracer experiments (e.g. 13C and 15N used simultaneously).

• lipidr lipidr an easy-to-use R package implementing a complete workflow for downstream analysis of lipidomics data. lipidr parses results exported from Skyline directly into R, allowing integration into current analysis frameworks. lipidr allows data inspection, normalization, univariate and multivariate analysis, displaying informative visualizations. lipidr also implements a novel Lipid Set Enrichment Analysis (LSEA), harnessing molecular information such as lipid class, chain length and unsaturation.

• mbkmeans Implements the mini-batch k-means algorithm for large datasets, including support for on-disk data representation.

• Melissa Melissa is a Baysian probabilistic model for jointly clustering and imputing single cell methylomes. This is done by taking into account local correlations via a Generalised Linear Model approach and global similarities using a mixture modelling approach.

• metagene2 This package produces metagene plots to compare coverages of sequencing experiments at selected groups of genomic regions. It can be used for such analyses as assessing the binding of DNA-interacting proteins at promoter regions or surveying antisense transcription over the length of a gene. The metagene2 package can manage all aspects of the analysis, from normalization of coverages to plot facetting according to experimental metadata. Bootstraping analysis is used to provide confidence intervals of per-sample mean coverages.

• miRspongeR This package provides several functions to study miRNA sponge (also called ceRNA or miRNA decoy), including popular methods for identifying miRNA sponge interactions, and the integrative method to integrate miRNA sponge interactions from different methods, as well as the functions to validate miRNA sponge interactions, and infer miRNA sponge modules, conduct enrichment analysis of modules, and conduct survival analysis of modules.

• mnem Mixture Nested Effects Models (mnem) is an extension of Nested Effects Models and allows for the analysis of single cell perturbation data provided by methods like Perturb-Seq (Dixit et al., 2016) or Crop-Seq (Datlinger et al., 2017). In those experiments each of many cells is perturbed by a knock-down of a specific gene, i.e. several cells are perturbed by a knock-down of gene A, several by a knock-down of gene B, … and so forth. The observed read-out has to be multi-trait and in the case of the Perturb-/Crop-Seq gene are expression profiles for each cell. mnem uses a mixture model to simultaneously cluster the cell population into k clusters and and infer k networks causally linking the perturbed genes for each cluster. The mixture components are inferred via an expectation maximization algorithm.

• Modstrings Representing nucleotide modifications in a nucleotide sequence is usually done via special characters from a number of sources. This represents a challenge to work with in R and the Biostrings package. The Modstrings package implements this functionallity for RNA and DNA sequences containing modified nucleotides by translating the character internally in order to work with the infrastructure of the Biostrings package. For this the ModRNAString and ModDNAString classes and derivates and functions to construct and modify these objects despite the encoding issues are implemenented. In addition the conversion from sequences to list like location information (and the reverse operation) is implemented as well.

• MOFA Multi-Omics Factor Analysis: an unsupervised framework for the integration of multi-omics data sets.

• nanotatoR Whole genome sequencing (WGS) has successfully been used to identify single-nucleotide variants (SNV), small insertions and deletions and, more recently, small copy number variants. However, due to utilization of short reads, it is not well suited for identification of structural variants (SV) and the majority of SV calling tools having high false positive and negative rates.Optical next-generation mapping (NGM) utilizes long fluorescently labeled native-state DNA molecules for de novo genome assembly to overcome the limitations of WGS. NGM allows for a significant increase in SV detection capability. However, accuracy of SV annotation is highly important for variant classification and filtration to determine pathogenicity.Here we create a new tool in R, for SV annotation, including population frequency and gene function and expression, using publicly available datasets. We use DGV (Database of Genomic Variants), to calculate the population frequency of the SVs identified by the Bionano SVCaller in the NGM dataset of a cohort of 50 undiagnosed patients with a variety of phenotypes. The new annotation tool, nanotatoR, also calculates the internal frequency of SVs, which could be beneficial in identification of potential false positive or common calls. The software creates a primary gene list (PG) from NCBI databases based on patient phenotype and compares the list to the set of genes overlapping the patient’s SVs generated by SVCaller, providing analysts with an easy way to identify variants affecting genes in the PG. The output is given in an Excel file format, which is subdivided into multiple sheets based on SV type. Users then have a choice to filter SVs using the provided annotation for identification of inherited, de novo or rare variants. nanotatoR provides integrated annotation and the expression patterns to enable users to identify potential pathogenic SVs with greater precision and faster turnaround times.

• NBAMSeq High-throughput sequencing experiments followed by differential expression analysis is a widely used approach to detect genomic biomarkers. A fundamental step in differential expression analysis is to model the association between gene counts and covariates of interest. NBAMSeq a flexible statistical model based on the generalized additive model and allows for information sharing across genes in variance estimation.

• netboost Boosting supported network analysis for high-dimensional omics applications. This package comes bundled with the MC-UPGMA clustering package by Yaniv Loewenstein.

• ngsReports This package provides methods and object classes for parsing FastQC reports and output summaries from other NGS tools into R, as well as visualising the data loaded from these files.

• OmicsLonDA Statistical method that provides robust identification of time intervals where omics features (such as proteomics, lipidomics, metabolomics, transcriptomics, microbiome, as well as physiological parameters captured by wearable sensors such as heart rhythm, body temperature, and activity level) are significantly different between groups.

• OVESEG An R package for multiple-group comparison to detect tissue/cell-specific marker genes among subtypes. It provides functions to compute OVESEG-test statistics, derive component weights in the mixture null distribution model and estimate p-values from weightedly aggregated permutations. Obtained posterior probabilities of component null hypotheses can also portrait all kinds of upregulation patterns among subtypes.

• PAIRADISE This package implements the PAIRADISE procedure for detecting differential isoform expression between matched replicates in paired RNA-Seq data.

• PAST PAST takes GWAS output and assigns SNPs to genes, uses those genes to find pathways associated with the genes, and plots pathways based on significance. Implements methods for reading GWAS input data, finding genes associated with SNPs, calculating enrichment score and significance of pathways, and plotting pathways.

• pathwayPCA Apply the Supervised PCA and Adaptive, Elastic-Net, Sparse PCA methods to extract principal components from each pathway. Use these pathway- specific principal components as the design matrix relating the response to each pathway. Return the model fit statistic p-values, and adjust these values for False Discovery Rate. Return a data frame of the pathways sorted by their adjusted p-values. This package has corresponding vignettes hosted in the ‘‘User Guides’’ page of https://gabrielodom.github.io/pathwayPCA/index.html, and the website for the development information is hosted at https://github.com/gabrielodom/pathwayPCA.

• PCAtools Principal Components Analysis (PCA) is a very powerful technique that has wide applicability in data science, bioinformatics, and further afield. It was initially developed to analyse large volumes of data in order to tease out the differences/relationships between the logical entities being analysed. It extracts the fundamental structure of the data without the need to build any model to represent it. This ‘summary’ of the data is arrived at through a process of reduction that can transform the large number of variables into a lesser number that are uncorrelated, i.e., the principal components, whilst at the same time being capable of easy interpretation on the original data.

• phemd Package for comparing and generating a low-dimensional embedding of multiple single-cell samples.

• pipeFrame pipeFrame is an R package for building a componentized bioinformatics pipeline. Each step in this pipeline is wrapped in the framework, so the connection among steps is created seamlessly and automatically. Users could focus more on fine-tuning arguments rather than spending a lot of time on transforming file format, passing task outputs to task inputs or installing the dependencies. Componentized step elements can be customized into other new pipelines flexibly as well. This pipeline can be split into several important functional steps, so it is much easier for users to understand the complex arguments from each step rather than parameter combination from the whole pipeline. At the same time, componentized pipeline can restart at the breakpoint and avoid rerunning the whole pipeline, which may save a lot of time for users on pipeline tuning or such issues as power off or process other interrupts.

• PoTRA The PoTRA analysis is based on topological ranks of genes in biological pathways. PoTRA can be used to detect pathways involved in disease (Li, Liu & Dinu, 2018). We use PageRank to measure the relative topological ranks of genes in each biological pathway, then select hub genes for each pathway, and use Fishers Exact test to determine if the number of hub genes in each pathway is altered from normal to cancer (Li, Liu & Dinu, 2018). Alternatively, if the distribution of topological ranks of gene in a pathway is altered between normal and cancer, this pathway might also be involved in cancer (Li, Liu & Dinu, 2018). Hence, we use the Kolmogorov–Smirnov test to detect pathways that have an altered distribution of topological ranks of genes between two phenotypes (Li, Liu & Dinu, 2018). PoTRA can be used with the KEGG, Biocarta, Reactome, NCI, SMPDB and PharmGKB databases from the devel graphite library.

• pram Publicly available RNA-seq data is routinely used for retrospective analysis to elucidate new biology. Novel transcript discovery enabled by large collections of RNA-seq datasets has emerged as one of such analysis. To increase the power of transcript discovery from large collections of RNA-seq datasets, we developed a new R package named Pooling RNA-seq and Assembling Models (PRAM), which builds transcript models in intergenic regions from pooled RNA-seq datasets. This package includes functions for defining intergenic regions, extracting and pooling related RNA-seq alignments, predicting, selected, and evaluating transcript models.

• PrecisionTrialDrawer A suite of methods to design umbrella and basket trials for preision oncology.

• PrInCE PrInCE (Predicting Interactomes from Co-Elution) uses a naive Bayes classifier trained on dataset-derived features to recover protein-protein interactions from co-elution chromatogram profiles. This package contains the R implementation of PrInCE.

• proBatch The proBatch package facilitates batch effects analysis and correction in high-thoughput experiments. It was developed primarily for mass-spectrometry proteomics (DIA/SWATH), but could also be applicable to most omic data with minor adaptations. The package contains functions for diagnostics (proteome/genome-wide and feature-level), correction (normalization and batch effects correction) and quality control. Non-linear fitting based approaches were also included to deal with complex, mass spectrometry-specific signal drifts.

• profileplyr Quick and straighforward visualization of read signal over genomic intervals is key for generating hypotheses from sequencing data sets (e.g. ChIP-seq, ATAC-seq, bisulfite/methyl-seq). Many tools both inside and outside of R and Bioconductor are available to explore these types of data, and they typically start with a bigWig or BAM file and end with some representation of the signal (e.g. heatmap). profileplyr leverages many Bioconductor tools to allow for both flexibility and additional functionality in workflows that end with visualization of the read signal.

• projectR Functions for the projection of data into the spaces defined by PCA, CoGAPS, NMF, correlation, and clustering.

• qckitfastq Assessment of FASTQ file format with multiple metrics including quality score, sequence content, overrepresented sequence and Kmers.

• qsmooth Smooth quantile normalization is a generalization of quantile normalization, which is average of the two types of assumptions about the data generation process: quantile normalization and quantile normalization between groups.

• RCM Combine ideas of log-linear analysis of contingency table, flexible response function estimation and empirical Bayes dispersion estimation for explorative visualization of microbiome datasets. The package includes unconstrained as well as constrained analysis.

• Rcwl The package can be a simple and user-friendly way to manage command line tools and build data analysis pipelines in R using Common Workflow Language (CWL).

• RcwlPipelines A collection of Bioinformatics pipeline recipes based on Rcwl.

• RepViz RepViz enables the view of a genomic region in a simple and efficient way. RepViz allows simultaneous viewing of both intra- and intergroup variation in sequencing counts of the studied conditions, as well as their comparison to the output features (e.g. identified peaks) from user selected data analysis methods.The RepViz tool is primarily designed for chromatin data such as ChIP-seq and ATAC-seq, but can also be used with other sequencing data such as RNA-seq, or combinations of different types of genomic data.

• Rhisat2 An R interface to the HISAT2 spliced short-read aligner by Kim et al. (2015). The package contains wrapper functions to create a genome index and to perform the read alignment to the generated index.

• rmelting R interface to the MELTING 5 program (https://www.ebi.ac.uk/biomodels/tools/melting/) to compute melting temperatures of nucleic acid duplexes along with other thermodynamic parameters.

• rScudo SCUDO (Signature-based Clustering for Diagnostic Purposes) is a rank-based method for the analysis of gene expression profiles for diagnostic and classification purposes. It is based on the identification of sample-specific gene signatures composed of the most up- and down-regulated genes for that sample. Starting from gene expression data, functions in this package identify sample-specific gene signatures and use them to build a graph of samples. In this graph samples are joined by edges if they have a similar expression profile, according to a pre-computed similarity matrix. The similarity between the expression profiles of two samples is computed using a method similar to GSEA. The graph of samples can then be used to perform community clustering or to perform supervised classification of samples in a testing set.

• scAlign An unsupervised deep learning method for data alignment, integration and estimation of per-cell differences in -omic data (e.g. gene expression) across datasets (conditions, tissues, species). See Johansen and Quon (2019) <doi:10.1101/504944> for more details.

• scds In single cell RNA sequencing (scRNA-seq) data combinations of cells are sometimes considered a single cell (doublets). The scds package provides methods to annotate doublets in scRNA-seq data computationally.

• scMerge Like all gene expression data, single-cell RNA-seq (scRNA-Seq) data suffers from batch effects and other unwanted variations that makes accurate biological interpretations difficult. The scMerge method leverages factor analysis, stably expressed genes (SEGs) and (pseudo-) replicates to remove unwanted variations and merge multiple scRNA-Seq data. This package contains all the necessary functions in the scMerge pipeline, including the identification of SEGs, replication-identification methods, and merging of scRNA-Seq data.

• scRecover scRecover is an R package for imputation of single-cell RNA-seq (scRNA-seq) data. It will detect and impute dropout values in a scRNA-seq raw read counts matrix while keeping the real zeros unchanged, since there are both dropout zeros and real zeros in scRNA-seq data. By combination with scImpute, SAVER and MAGIC, scRecover not only detects dropout and real zeros at higher accuracy, but also improve the downstream clustering and visualization results.

• scTensor The algorithm is based on the non-negative tucker decomposition (NTD) of nnTensor.

• sitePath The package does hierarchical search for fixation events given multiple sequence alignment and phylogenetic tree. These fixation events can be specific to a phylogenetic lineages or shared by multiple lineages.

• SMAD Assigning probability scores to prey proteins captured in affinity purification mass spectrometry (AP-MS) expriments to infer protein- protein interactions. The output would facilitate non-specific background removal as contaminants are commonly found in AP-MS data.

• SpatialCPie SpatialCPie is an R package designed to facilitate cluster evaluation for spatial transcriptomics data by providing intuitive visualizations that display the relationships between clusters in order to guide the user during cluster identification and other downstream applications. The package is built around a shiny “gadget” to allow the exploration of the data with multiple plots in parallel and an interactive UI. The user can easily toggle between different cluster resolutions in order to choose the most appropriate visual cues.

• SpectralTAD SpectralTAD is an R package designed to identify Topologically Associated Domains (TADs) from Hi-C contact matrices. It uses a modified version of spectral clustering that uses a sliding window to quickly detect TADs. The function works on a range of different formats of contact matrices and returns a bed file of TAD coordinates. The method does not require users to adjust any parameters to work and gives them control over the number of hierarchical levels to be returned.

• sRACIPE sRACIPE implements a randomization-based method for gene circuit modeling. It allows us to study the effect of both the gene expression noise and the parametric variation on any gene regulatory circuit (GRC) using only its topology, and simulates an ensemble of models with random kinetic parameters at multiple noise levels. Statistical analysis of the generated gene expressions reveals the basin of attraction and stability of various phenotypic states and their changes associated with intrinsic and extrinsic noises. sRACIPE provides a holistic picture to evaluate the effects of both the stochastic nature of cellular processes and the parametric variation.

• ssrch Demonstrate tokenization and a search gadget for collections of CSV files.

• Structstrings The Structstrings package implements the widely used dot bracket annotation for storing base pairing information in structured RNA. Structstrings uses the infrastructure provided by the Biostrings package and derives the DotBracketString and related classes from the BString class. From these, base pair tables can be produced for in depth analysis. In addition, the loop indices of the base pairs can be retrieved as well. For better efficiency, information conversion is implemented in C, inspired to a large extend by the ViennaRNA package.

• StructuralVariantAnnotation StructuralVariantAnnotation contains useful helper functions for dealing with structural variants in VCF format. The packages contains functions for parsing VCFs from a number of popular callers as well as functions for dealing with breakpoints involving two separate genomic loci encoded as GRanges objects.

• SubCellBarCode Mass-Spectrometry based spatial proteomics have enabled the proteome-wide mapping of protein subcellular localization (Orre et al. 2019, Molecular Cell). SubCellBarCode R package robustly classifies proteins into corresponding subcellular localization.

• survtype Subtypes are defined as groups of samples that have distinct molecular and clinical features. Genomic data can be analyzed for discovering patient subtypes, associated with clinical data, especially for survival information. This package is aimed to identify subtypes that are both clinically relevant and biologically meaningful.

• SynMut There are increasing demands on designing virus mutants with specific dinucleotide or codon composition. This tool can take both dinucleotide preference and/or codon usage bias into account while designing mutants. It is a powerful tool for in silico designs of DNA sequence mutants.

• TNBC.CMS This package implements a machine learning-based classifier for the assignment of consensus molecular subtypes to TNBC samples. It also provides functions to summarize genomic and clinical characteristics.

• topconfects Find the largest confident effect sizes from a large collection, while maintaining False Discovery Rate and False Coverage-statement Rate control. The main application is differential gene expression analysis, providing genes ranked in order of confident log2 fold change.

• TPP2D FDR-controlled analysis of 2D-TPP experiments by functional analysis of dose-response curves across temperatures.

• TreeSummarizedExperiment TreeSummarizedExperiment has extended SingleCellExperiment to include hierarchical information on the rows or columns of the rectangular data.

• VCFArray VCFArray extends the DelayedArray to represent VCF data entries as array-like objects with on-disk / remote VCF file as backend. Data entries from VCF files, including info fields, FORMAT fields, and the fixed columns (REF, ALT, QUAL, FILTER) could be converted into VCFArray instances with different dimensions.

• VennDetail A set of functions to generate high-resolution Venn,Vennpie plot,extract and combine details of these subsets with user datasets in data frame is available.

• Xeva Contains set of functions to perform analysis of patient-derived xenograft (PDX) data.

New Data Experiment Packages

There are 13 new data experiment packages in this release of Bioconductor.

• adductData mzXML files from Grigoryan et al 2016 (Anal Chem).

• bodymapRat This package contains a SummarizedExperiment from the Yu et al. (2013) paper that performed the rat BodyMap across 11 organs and 4 developmental stages. Raw FASTQ files were downloaded and mapped using STAR. Data is available on ExperimentHub as a data package.

• chipseqDBData Sorted and indexed BAM files for ChIP-seq libraries, for use in the chipseqDB workflow. BAM indices are also included.

• CluMSIDdata This package contains various LC-MS/MS and GC-MS data that is used in vignettes and examples in the CluMSID package.

• curatedAdipoChIP A curated dataset of publicly available ChIP-sequencing of transcription factors, chromatin remodelers and histone modifications in the 3T3-L1 pre-adipocyte cell line. The package document the data collection, pre-processing and processing of the data. In addition to the documentation, the package contains the scripts that was used to generated the data.

• curatedAdipoRNA A curated dataset of RNA-Seq samples. The samples are MDI-induced pre-phagocytes (3T3-L1) at different time points/stage of differentiation. The package document the data collection, pre-processing and processing. In addition to the documentation, the package contains the scripts that was used to generated the data.

• FlowSorted.CordBloodCombined.450k Raw data objects to be used for umbilical cord blood cell proportion estimation in minfi and similar packages. The FlowSorted.CordBloodCombined.450k object is based in samples assayed by Bakulski et al, Gervin et al., de Goede et al., and Lin et al.

• HCAData This package allows a direct access to the dataset generated by the Human Cell Atlas project for further processing in R and Bioconductor, in the comfortable format of SingleCellExperiment objects (available in other formats here: http://preview.data.humancellatlas.org/).

• macrophage This package provides the output of running Salmon on a set of 24 RNA-seq samples from Alasoo, et al. “Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response”, published in Nature Genetics, January 2018. For details on version numbers and how the samples were processed see the package vignette.

• MOFAdata A collection of datasets to accompany the R package MOFA and illustrate running and analysing MOFA models.

• nanotubes Cap Analysis of Gene Expression (CAGE) data from “Identification of Gene Transcription Start Sites and Enhancers Responding to Pulmonary Carbon Nanotube Exposure in Vivo” by Bornholdt et al. supplied as CAGE Transcription Start Sites (CTSSs).

• NestLink Provides next-generation sequencing (NGS) and mass spectrometry (MS) sample data, code snippets and replication material used for developing NestLink. The NestLink approach is a protein binder selection and identification technology able to biophysically characterize thousands of library members at once without handling individual clones at any stage of the process. Data were acquired on NGS and MS platforms at the Functional Genomics Center Zurich.

• oct4 This package provides the output of running Salmon on a set of 12 RNA-seq samples from King & Klose, “The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells”, published in eLIFE, March 2017. For details on version numbers and how the samples were processed see the package vignette.

New Workflows

There are 4 new workflow packages in this release of Bioconductor.

• BgeeCall Reference intergenic regions are generated by the Bgee RNA-Seq pipeliene. These intergenic regions are used to generate all Bgee RNA-Seq present/absent expression calls. This package now allows to generate your own present/absent calls using both these intergenic regions and the expertise of Bgee, as long as your species is present in Bgee. The threshold of present/absent expression is no longer arbitrary defined but is calculated based on expression of all RNA-Seq libraries integrated in Bgee.

• CAGEWorkflow Workflow for analyzing Cap Analysis of Gene Expression (CAGE) data using R/Bioconductor.

• csawUsersGuide A user’s guide for the csaw package for detecting differentially bound regions in ChIP-seq data. Describes how to read in BAM files to obtain a per-window count matrix, filtering to obtain high-abundance windows of interest, normalization of sample-specific biases, testing for differential binding, consolidation of per-window results to obtain per-region statistics, and annotation and visualization of the DB results.

• SingscoreAMLMutations This workflow package shows how transcriptomic signatures can be used to infer phenotypes. The workflow begins by showing how the TCGA AML transcriptomic data can be downloaded and processed using the TCGAbiolinks packages. It then shows how samples can be scored using the singscore package and signatures from the MSigDB. Finally, the predictive capacity of scores in the context of predicting a specific mutation in AML is shown.The workflow exhibits the interplay of Bioconductor packages to achieve a gene-set level analysis.

NEWS from new and existing Software Packages

ACE

             Changes in version 1.1.2 (2019-04-23)                  

• added citation information!

• fixed bug in getadjustedsegments and twosamplecompare with non-matching NAs

             Changes in version 1.1.1 (2018-11-13)                  
  

• added forcesegmentsontemplate function

• speed boost by small coding change in model fitting

• added argument in loopsquaremodel to make returning the models optional and flexible (see documentation)

ADAM

            Changes in version 0.99.66 (2018-11-15)                 

• Fixed possible problem to access kegg id

            Changes in version 0.99.65 (2018-11-05)                 
  

• Fixed possible bugs

             Changes in version 0.99.0 (2018-10-05)                 
  

• Submitted to Bioconductor

AffiXcan

                    Changes in version 1.1.3                        

BUG FIXES

• Fix a bug in generating the vignette for ‘devel’ version of Bioconductor

alevinQC

                   Changes in version 0.99.0                        

• Preparation for Bioconductor submission

                    Changes in version 0.1.0                        
  

• Initial version

amplican

                    Changes in version 1.5.8                        

• amplican has been published now, doi: 10.1101/gr.244293.118

• clearly outperforms other tools on many benchmarks

• please cite the paper if you ar eusing amplican

AneuFinder

                   Changes in version 1.11.1                        

BUG FIXES

• Fixed “object ‘dfplot.seg’ not found” bug when building vignette.

AnnotationHub

                   Changes in version 2.15.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• (2.15.9) The Hubs have been updated to use BiocFileCache as a backend utility for managing and downloading resources. This allows for file specific caching mechanism. This change is a significant user change as it changed the default directories for the Hubs (AnnotationHub/ExperimentHub) as well as the base directory no longer being hidden.

NEW FEATURES

• (2.15.15) Added BamFile Resource method

• (2.15.9) Add helper function to get additional information on resources. getInfoOnIds

• (2.15.2) Add function to list currently available DispatchClass

USER-VISIBLE MODIFICATIONS

• (2.15.3) Bioconductor will no longer accept random, Individual resources without an accompanied package.

• (2.15.4) We also encourage the use of AnnotationHub rather than very large annotation packages. We added sections for users wishing to convert existing packages to use AnnotationHub as well.

• (2.15.7) There were substantial updates to Rsamtools. Rsamtools no longer supports razip files. These files have been removed from the hub and vignette updated to use the twobit and gff files

BUG FIXES

• (2.15.5) Fixed bug. If resources are removed from the hub, this should only be reflected in the devel branch but still be available in release branch. The filter for exposed resources was refined to respect datadateremoved

AnnotationHubData

                   Changes in version 1.13.0                        

NEW FEATURES

• Added ability to have multiple RDataPaths associated with single hub id for strongly associated files (like bam and its bai index file)

• DispatchClass are now validated against AnnotationHub::DispatchClassList() which contains currently available DispatchClass and brief description of loading process.

anota2seq

                    Changes in version 1.5.0                        

• We added a new option to the output parameter of the anota2seqGetOutput function, more details can be found in the function help.

• The quality control section of the vignette has been expanded with more details, furthermore we added an example of quality control of poorly normalized data as reference.

• We removed the apvSlope and apvSlopeP columns from the output of analysis for total mRNA and translated mRNA as these values are not generated for RNA source differential expression analysis.

apeglm

                    Changes in version 1.5.4                        

• Added possibility for weights and standard errors to bbEstDisp(). The standard errors are for the log of dispersion (theta).

ASICS

                     Changes in version 2.0                         

New features

• preprocessing functions from PepsNMR package

Improvements

• changes in alignment function

• new step to improve library alignment and thus quantifications

AssessORF

             Changes in version 1.1.7 (2019-04-29)                  

• Added a function, CompareAssessmentResults, for comparing two results objects against each other

• Added a processors parameter to MapAssessmentData for compatibility with DECIPHER functions

             Changes in version 1.1.6 (2019-04-07)                  
  

• Added parameters to AssessGenes to bound the range in which to look for conserved starts that can serve as alternative options to a predicted start

• Added a parameter to AssessGenes that requires ORFs with protein evidence but no predicted start to have a certain minimum number of peptide hits in order to be included in the final output

             Changes in version 1.1.5 (2019-01-11)                  
  

• Update to how conserved starts and conserved stops are utilized in AssessGenes

• Removed weighted score

• Made clarifications to the man pages

• Minor edits to the vignette

             Changes in version 1.1.4 (2018-12-15)                  
  

• Updated AssessGenes to make sure predicted stops are valid for their corresponding genes, and users will be warned appropriately if a predicted stop is invalid

• Minor updates to plots

• Bug fixes on previous version’s MapAssessmentData updates

             Changes in version 1.1.3 (2018-11-12)                  
  

• Fixed a bug affecting coverage related to gaps in alignments in MapAssessmentData

• Used exponential moving averages to filter out bad alignment regions in MapAssessmentData

                    Changes in version 1.1.2                        
  

• Implemented a fix to the vignette so it builds without an internet connection

                    Changes in version 1.1.1                        
  

• Reduced time it takes to run MapAssessmentData examples # AssessORF 0.99

ATACseqQC

                    Changes in version 1.7.8                        

• change the function of footprintsScanner.

                    Changes in version 1.7.7                        
  

• add parameter outPath for splitGAlignmentsByCut.

                    Changes in version 1.7.6                        
  

• fix a bug in PTscore.

                    Changes in version 1.7.5                        
  

• use file.copy instead of file.rename.

                    Changes in version 1.7.4                        
  

• add parameter outbam for shiftGAlignmentsList.

                    Changes in version 1.7.3                        
  

• Update documentation for Transcription start site (TSS) enrichment values

                    Changes in version 1.7.2                        
  

• add the new biocViews tag “ImmunoOncology”

                    Changes in version 1.7.1                        
  

• add more documentation for bigFile parameter in readBamFile.R

atSNP

             Changes in version 0.99.0 (2018-12-29)                 

• Submitted to Bioconductor

AUCell

                     Changes in version 1.5                         

• Added function orderAUC()

• Error fixes in AUCell_plotTSNE()

BANDITS

                    Changes in version 1.0.0                        

• Submitted to Bioconductor

BASiCS

             Changes in version 1.5.34 (2019-04-20)                 

• Fixes typo in vignette

             Changes in version 1.5.33 (2019-04-19)                 
  

• Updated ERCC formula in the vignette.

             Changes in version 1.5.32 (2019-04-17)                 
  

• Minor change in BASiCS_MCMC to avoid storing adaptive variances in the BASiCS_Chain object when StoreAdapt = TRUE.

• New unit test to ensure the correct output in BASiCS_Chain@parameters

• Minor change in Summary method for BASiCS_Chain class to avoid calculating posterior summaries when designMatrix is part of the parameters slot

• Added return to the docummentation of BASiCS_effectiveSize.

             Changes in version 1.5.31 (2019-04-15)                 
  

• Updated vignette to include ERCC calculation

             Changes in version 1.5.30 (2019-04-11)                 
  

• BASiCS_effectiveSize has been created as a wrapper of coda::effectiveSize. This is to resolve issues when Param = 'epsilon' as it contains NA for very lowly expressed genes that are excluded from the mean/over-dispersion trend.

             Changes in version 1.5.29 (2019-04-10)                 
  

• Unit test associated to BASiCS_Sim updated to use a fixed seed and to check exact values being reproducible

             Changes in version 1.5.28 (2019-04-09)                 
  

• Edited version of BASiCS_Sim to allow no spikes and multiple batches

• Documentation updated accordingly

             Changes in version 1.5.27 (2019-04-08)                 
  

• Edits BASiCS_TestDE to avoid low posterior probability thresholds derived from the EFDR calibration. This alters some of the related ‘Hidden’ functions.

• In BASiCS_TestDE, default values for EFDR_M, EFDR_D and EFDR_R were changed to 0.05.

• Unit tests updated accordingly

             Changes in version 1.5.26 (2019-04-08)                 
  

• Similar changes applied to utils_MCMCcppReg.cpp and utils_MCMCcppRegNoSpikes.cpp.

             Changes in version 1.5.25 (2019-04-07)                 
  

• Minor change in muUpdateNoSpikes (C++ function in utils_MCMCNoSpikes.cpp) to avoid WARNINGS in bioc-devel related to integers vs unsigned integers

             Changes in version 1.5.24 (2019-04-05)                 
  

• Minor edit to the documentation of makeExampleBASiCS_Data (fixed link to set.seed documentation as it led to WARNINGS in Bioc-devel)

             Changes in version 1.5.23 (2019-04-02)                 
  

• Minor edit to the documentation of makeExampleBASiCS_Data (explain why a fixed seed is no longer used)

             Changes in version 1.5.22 (2019-04-02)                 
  

• HiddenCheckValidCombination, HiddenGeneParams and HiddenGeneParams moved from Methods.R to HiddenUtils.R

• sapply replaced by vapply in HiddenCheckValidCombination, HiddenThresholdSearchDetectHVL_LVG.R and HiddenThresholdSearchTestDE.R

• Use of set.seed removed from makeExampleBASiCS_Data

• Unit tests updated accordingly

• Adds missing running examples to Rds in order to pass R CMD BioCheck

             Changes in version 1.5.21 (2019-04-01)                 
  

• Uses built-in chain in examples for BASiCS_diagHist and BASiCS_diagPlot

             Changes in version 1.5.20 (2019-04-01)                 
  

• Updated documentation for BASiCS_MCMC, BASiCS_DetectHVG, BASiCS_DetectLVG and BASiCS_VarThresholdSearchHVG_LVG

             Changes in version 1.5.19 (2019-03-31)                 
  

• stats4 added to imports in order to import plot S4 generic.

• KernSmooth removed from DESCRIPTION.

• Maintainer field removed from DESCRIPTION (use Author@R only)

• Updates to travis integration to include BiocCheck

             Changes in version 1.5.17 (2019-03-30)                 
  

• Minor changes in dependencies to pass R CMD check

• Minor typo fix in documentation of newBASiCS_Data

• @export call added to all methods

             Changes in version 1.5.16 (2019-03-30)                 
  

• SingleCellExperiment moved to depends (DESCRIPTION)

• Explicit calls to external packages (e.g. SingleCellExperiment::)

• Unit tests for BASiCS_diagHist and BASiCS_diagPlot

• BASiCS_diagHist, BASiCS_diagPlot and BASiCS_showFit moved from methods to functions

• Internal functions marked as ‘Hidden’

• BASiCS_diagHist, etc moved into separate .R files

             Changes in version 1.5.15 (2019-03-27)                 
  

• Extended message to suggest additional QC when MCMC sampler fails

             Changes in version 1.5.14 (2019-03-27)                 
  

• Brackets removed from setGeneric call (as per Hadley Wickham recommendation)

• Removes full import of ggplot2 in BASiCS_Package.R

• BASiCS_Package.R is now in alphabetical order

             Changes in version 1.5.13 (2019-03-27)                 
  

• BASiCS_D_TestDE from deprecated to defunct (follows BioC guidelines)

             Changes in version 1.5.12 (2019-03-26)                 
  

• R (>= 3.6) is now a requirement

             Changes in version 1.5.11 (2019-03-26)                 
  

• Edits in BASiCS_Package.R so that roxygen2 creates NAMESPACE

• testthat moved from Imports to Suggests

             Changes in version 1.5.10 (2019-03-26)                 
  

• Corrected ordering in TestDE outpout so that genenames always match

• Small fixes for R CMD check

• Ordering in BASiCS_DetectHVG and BASiCS_DetectLVG can only be done on GeneNames, GeneIndex and Prob

             Changes in version 1.5.9 (2019-03-24)                  
  

• Alan O’Callaghan is now author

• diagPlot and diagHist methods added to facilitate diagnosis of convergence and mixing for MCMC chains

• Added explicit calls to ggplot2 in plot methods.

• BASiCS_DetectHVG and BASiCS_DetectLVG edited based on the “regression” approach (i.e. using epsilon to detect HVGs/LVGs).

• In BASiCS_DetectHVG and BASiCS_DetectLVG, options for OrderVariable were simplified (only original order and based on probability)

• Temporary changes in no-spikes version have been restored

             Changes in version 1.5.8 (2019-03-22)                  
  

• Changes DESCRIPTION to have a single maintainer

• Density plot added to plot Method for BASiCS_Chain objects

• Output plots for plot Method for BASiCS_Chain objects

             Changes in version 1.5.7 (2019-03-22)                  
  

• Added default value for ‘BatchInfo’ within ‘BASiCS_MCMC’

                    Changes in version 1.5.6                        
  

• Bug fix when not providing BatchInfo as factor

• Extra check if batch names contain spaces

• Added line breaks after individual error messages

• Bug fix that corrects for the number of factors in BatchInfo vector

• Small bug fix in ‘test_mcmc_arguments.R’

             Changes in version 1.5.5 (2019-03-14)                  
  

• Updated vignette to include recommended settings earlier.

             Changes in version 1.5.4 (2019-02-12)                  
  

• Replaces HPDinterval by coda::HPDinterval in BASiCS_showFit method

• Same as above when calling mcmc

• Changes BASiCS_showFit such that fit line is on top of the dots

• Additional optional arguments (markExcludedGenes, colour, GenesSel and colourGenesSel) added to BASiCS_showFit for more flexibility

             Changes in version 1.5.3 (2018-12-06)                  
  

• Removes ... argument from BASiCS_VarianceDecomp

• Adds missing argument (beside) to documentation of BASiCS_VarianceDecomp

             Changes in version 1.5.2 (2018-12-01)                  
  

• Fixes use of BatchInfo when it cannot be parsed to numeric

• Refactors the use of ... argument (several functions)

             Changes in version 1.5.1 (2018-11-29)                  
  

• ImmunoOncology added in biocViews as requested by BioC core team

bayNorm

                    Changes in version 1.1.6                        

• Suppress warning message came from BiocParallel.

                    Changes in version 1.1.4                        
  

• For a smoother progress bar, use foreach instead of BiocParallel.

bcSeq

                   Changes in version 1.5.11                        

• using new data structure for the library to speed up the mapping process.

                    Changes in version 1.5.9                        
  

• fix bugs in the examples

                    Changes in version 1.5.7                        
  

• fix bugs in the examples

                    Changes in version 1.5.3                        
  

• fix bugs in vignette for bioconductor new platform

beachmat

                    Changes in version 2.0.0                        

• Converted beachmat into a header-only library to simplify linking, avoid ABI incompatibilities.

• Minor API change for external native support to avoid using C++ classes with C-style linkage.

BEclear

             Changes in version 2.0.0 (2019-04-30)                  

• Code refactoring o Simplification of the source code o Changes to the API o Extraction of the preprocessing function o loss function is now exported o renaming of functions o Combination of calcPvals and calcMedians methods into one

• Documentation o Update of the README o New Vignette

• Serial execution of the methods is now the default

• Performance improvments o Usage of RCPP for further performance improvements

• Change from GPL-2 to GPL-3 license

• Removing of deprecated functions

• Tests o Implementation of further tests

bigPint

             Changes in version 0.99.7 (2019-01-28)                 

BigPint accepted to Bioconductor (Open source software for bioinformatics)

             Changes in version 0.99.0 (2018-09-30)                 

Vignette for bigPint was released on github.io

bioCancer

                   Changes in version 1.11.00                       

• Change the address of cgdsr: http://www.cbioportal.org/ instead http://www.cbioportal.org/public-portal/

BiocCheck

                    Changes in version 1.19                         

NEW FEATURES

• (1.19.33) Add Authors@R vs Author/Maintainer check

• (1.19.29) Add non evaluated code chunks that have not been executed because of invalid syntax (,R, r). Valid syntax for an evaluated code chunk takes the form{r} or ```{R}.

• (1.19.28) Check that vignette metadata set correctly

• (1.19.27) Check for Author@R or Author/Maintainer but not both

• (1.19.25) Check for use of remotes: in Description

• (1.19.18) Check for use of dontrun/donttest

• (1.19.15) Check vignetteEngine/vignetteBuilder minimially declared in Suggests

• (1.19.9) Check usage of donttest and dontrun in man page documentation

• (1.19.9) Update deprecated check to check for Bioconductor release and devel deprecated packages as specified in biocViews

• (1.19.7) More helpful ERROR when using a non valid command line option.

• (1.19.4) All checks module. Ability to turn on/off with flag options. See ‘R CMD BiocCheck –help’

• (1.19.1) New Check options to turn off if in CRAN (–no-check-CRAN) and Bioconductor mailing list and support site (–no-check-bioc-help)

USER SIGNIFICANT CHANGES

• (1.19.8) Updated Documentation in vignette for flag/option controls and reorganization of code/checks. Grouped similar checks together and changed order of checks.

• (1.19.3) Remove Native Routine Registrations (use flag in R CMD check instead R_CHECK_NATIVE_ROUTINE_REGISTRATION)

• (1.19.2) Match CRAN standards of package size <= 5MB (updated from 4MB)

BUG FIXES

• (1.19.26) Fix NEWS check to recognize NEWS.md

• (1.19.26) Check all repos for existing package not just software

• (1.19.23) Informative message if no biocViews term found

• (1.19.22) Fix output of system2 usage check

• (1.19.19) Test only closures for T/F

• (1.19.14) Fix ERROR when more than one VignetteEngine found

• (1.19.10) Add suggestion of FormatR package to formatting notes

• (1.19.10) Fix function lengths to be a NOTE and only display if functions are greater than 50 lines long.

• (1.19.6) Replace use of devtools::create with usethis::create_package as function was deprecated.

• (1.19.5) Fix length > 1 logical comparison in if statement

BiocFileCache

                     Changes in version 1.7                         

BUG FIX

• (1.7.10) Fix date comparison to use as.POSIXlt instead of as.Date. This catches the rare edge case if a remote resource is updated twice in a day and a download happened in between the two.

• (1.7.9) Make creation of database atomic commits

• (1.7.8) Make adding resource to database atomic commits

• (1.7.4) Limit where possible opening database in RW mode. Use read-only mode whereever possible to avoid database locking

• (1.7.2) Fix bug in multi path addition through bfcadd/bfcrpaths. The function was assuming all files had same rtype and action. Now can vectorize

• (1.7.1) Fix man documentation example. Interactive vs non interactive session

BiocNeighbors

                    Changes in version 1.2.0                        

• findNeighbors() and queryNeighbors() now accept a vector of point-specific thresholds.

• Added an VP tree implemention in findVptree(), queryVptree(), buildVptree(). Supported dispatch to these methods in the generics.

• Added a HNSW implementation in findHnsw(), queryHnsw(), buildHnsw(). Supported dispatch to these methods in the generics.

• Renamed buildNNIndex() to buildIndex().

• Converted findNeighbors() and queryNeighbors() into S4 methods. Created specific rangeFind() and rangeQuery() functions for KMKNN and VP tree algorithms.

• Modified AnnoyIndex class to hold the original data matrix. Created bnorder(), bndata() generics to obtain (possibly reordered) input matrices for all indexes.

• Supported Manhattan distance searching in all algorithms.

BiocParallel

                    Changes in version 1.18                         

USER VISIBLE CHANGES

• (v 1.17.6) Initial use of registered BPPARAM does not advance random number seed, see https://stat.ethz.ch/pipermail/bioc-devel/2019-January/014526.html

• (v 1.17.7) Loading package does not advance random number seed, see https://stat.ethz.ch/pipermail/bioc-devel/2019-January/014535.html

• (v. 1.17.7) removed deprecated functions bplasterror(), bpresume(), bpcatchError() and field catch.error.

• (v. 1.17.7) Make logdir, resultdir fields of BiocParallelParam.

• (v. 1.17.7) replaced internal use of BatchJobs:::checkDir() (testing existence and read / write ability of log and other directories) with BiocParallelParam validity check.

• (v. 1.17.7) expose ‘developer’ interface, ?DeveloperInterface

• (v. 1.17.11) on Windows, coerce MulticoreParam(n) to MulticoreParam(1) == SerialParam()`

BUG FIXES

• (v 1.17.4) port 1.16.3 (no ‘>’ on SnowParam() worker end) and 1.16.4 (bpRNGseed<-() accepts NULL)

• (v 1.17.5) port 1.16.4 (bpRNGseed() can reset seed to NULL), 1.16.5 (number of available cores defaults to 1 if cannot be determined).

biocViews

                   Changes in version 1.51.11                       

NEW FEATURES

• (1.51.7) Cross check views with manifest file so all expected bioconductor package get listed in biocViews. New argument to write_VIEWS manifestFile

• (1.51.9) New argument to write_VIEWS meatPath. For packages that fail to build on any platform, use cloned repository DESCRIPTION file to fill in as much information to the biocVIEWS entry.

• (1.51.10) Add new biocVIEW terms ImmunoOncolocy and ImmunoOncologyWorkflow.

• (1.51.12) Allow NEWS file to be in .md format. R 3.6 started allowing NEWS, NEWS.Rd and newly NEWS.md formats. Adjust code accordingly.

BioMM

                   Changes in version 0.99.13                       

• updated the format of NEWS

• updated BioMMtutorial.Rmd

• updated data4demo.R

• replaced the generation of stage-2 data by BioMMreconData() with preprocessed ‘stage2dataA’ to reduce runtime

• increased repeatA1 to 50 for BioMM() example to avoid any NAs.

• created stage2dataA.rds

                   Changes in version 0.99.12                       
  

• updated the format of NEWS

                   Changes in version 0.99.11                       
  

• updated DESCRIPTION file

                   Changes in version 0.99.10                       
  

• minor bug fixed in getDataAfterFS()

• updated installation method

                   Changes in version 0.99.9                        
  

• removed uncessary print statements

• removed ‘return’ calls for some functions

• removed unnecessary ‘which’ statements

• replaced the usage of MulticoreParam()

• updated tutorial with smaller examples and models with less computation

                   Changes in version 0.99.8                        
  

• updated author, maintainer section in DESCRIPTION

• updated parallel computing cores used in the vignettes

                   Changes in version 0.99.7                        
  

• updated parallel evaluation environments

• updated installation method in README.md

• more cores (non-windows) for parallel computing used in the vignettes to reduce runtime

                   Changes in version 0.99.6                        
  

• updated plotRankedFeature() and getMetrics()

• increased core number for parallel computing

• removed Duplicated descriptions in *.Rd files

                   Changes in version 0.99.5                        
  

• reformatted code by using formatR

• bplapply() instead of mclapply

• message() instead of print() for end-user messages

• improved usage of which()

• use seq_along() instead of seq_len(length())

• updated installation method

• renamed R source files

                   Changes in version 0.99.4                        
  

• updated example in BioMMreconData()

                   Changes in version 0.99.3                        
  

• updated example in BioMM()

                   Changes in version 0.99.2                        
  

• updated R version dependency (from 3.5.2 to 3.6)

• Removed the file LICENSE

                   Changes in version 0.99.1                        
  

• updated R version dependency (from 3.5.0 to 3.5.2)

                   Changes in version 0.99.0                        
  

• Removed the file “BioMM.Rproj”

biosigner

                   Changes in version 1.11.26                       

NEW FEATURE

• biosign and plot methods: ‘fig.pdfC’ and ‘info.txtC’ arguments have been added for compatibility reasons with other packages; they have the same role as ‘file.pdfC’ and ‘.sinkC’ which now generate a deprecated warning.

                   Changes in version 1.11.24                       
  

MINOR MODIFICATION

• minor internal modification

                   Changes in version 1.11.22                       
  

MINOR MODIFICATION

• minor internal modification

                   Changes in version 1.11.20                       
  

MINOR MODIFICATION

• minor internal modification

                   Changes in version 1.11.18                       
  

MINOR MODIFICATION

• minor internal modification

                   Changes in version 1.11.16                       
  

MINOR MODIFICATION

• minor internal modification for the handling of ExpressionSet instances

                   Changes in version 1.11.14                       
  

MINOR MODIFICATION

• minor internal modification

                   Changes in version 1.11.12                       
  

MINOR MODIFICATION

• minor modification in the example of application to ExpressionSet instances

                   Changes in version 1.11.10                       
  

MINOR MODIFICATION

• minor update of example

                   Changes in version 1.11.8                        
  

MINOR MODIFICATION

• vignette minor modification

                   Changes in version 1.11.6                        
  

MINOR MODIFICATION

• dev.new() is no more called by the plot method

                   Changes in version 1.11.4                        
  

BUG FIXED

• error message when y is a character but not a factor is now fixed

                   Changes in version 1.11.2                        
  

NEW FEATURES

• Application to ExpressionSet: tiers now returned in the fData

breakpointR

                    Changes in version 1.1.2                        

• Fixed bug in hotspotter function

• Improved handling of small chromosomes/contigs

• Fixed bug in masking certain genomic regions (maskRegions param)

• Improved handling of double SCE chromosomes when synchronizing read directionality across cells

BUMHMM

                    Changes in version 1.6.2                        

• Updated links to external functions in man pages.

CAGEfightR

                     Changes in version 1.5                         

• Added new functions for spatial analysis of clusters: findLinks finds nearby pairs of clusters (for example TSSs and enhancers) and calculates the correlation of expression between them. findStretches find stretches along the genome where clusters are within a certain distance of eachother (for example groups of enhancer forming a super enhancer) and calculates the average pairwise correlation between members.

• Changed the way clustering works: CAGEfightR uses coverage() to calculate genome-wide signals and now rounds the resulting signal to a certain number of digits (this can be modified via the CAGEfightR.round option), to prevent small positive or negative values due to floating point errors. This makes clustering more stable meaning the tuneTagClustering function is now deprecated. This should also increase the speed of most functions.

• CAGEfightR now uses GPos instead of GRanges for storing CTSSs, this should result in improved memory performance.

• Several changes to clusterBidirectionality: Balance is now calculated using the midpoint as well (preventing some rare cases where the midpoint could mask a single highly expressed CTSS), the pooled CTSS signal is now prefiltered for bidirectionality to increase speed and custom balance function can be provided (Bhattacharyya coefficient and Andersson’s D are included).

• Added new check-functions to make it easier to check if objects are formatted correctly

CAGEr

                   Changes in version 1.26.0                        

DOCUMENTATION

• Split the “CAGE resources” documentation into a separate vignette.

CAMERA

                   Changes in version 1.39.2                        

BUG FIXES

• Fix duplicate vignette name

canceR

                   Changes in version 1.17.6                        

• Remove dependency of RSvgDevice. This package is not available for Windows os.

• Remove GSEA.1.0.R from /data folder

                   Changes in version 1.17.5                        
  

• import from grDevice new.dev savePlot

• remove /data/datalist

• import RSvgDevice (not available for windows OS?)

                   Changes in version 1.17.4                        
  

• modify doc for cbind.na and rbind.na functiONs

                   Changes in version 1.17.3                        
  

• modify doc for cbind.na and rbind.na functiONs

Cardinal

                   Changes in version 2.1.30                        

BUG FIXES

• Fixed bug where ‘spatialShrunkenCentroids’ classification would change the user ‘options(Cardinal.progress)’

                   Changes in version 2.1.29                        
  

BUG FIXES

• Coercing to ‘SpatialShrunkenCentroids2’ now drops empty classes for segmentations (as expected)

                   Changes in version 2.1.28                        
  

BUG FIXES

• Fixed ‘topFeatures’ method for ‘SpatialShrunkenCentroids2’ where ‘statistic’ was actually printing the ‘centers’

• The ‘collect’ method for ‘MSProcessedImagingExperiment’ now preserves sparseness when pulling into memory

                   Changes in version 2.1.27                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Added ‘mzFilter’ as an alias for ‘peakFilter’ with more suitable defaults for non-peak-picked spectra

BUG FIXES

• Minor fixes to ‘print’ method for plots and images

• Minor fixes to margin padding for ‘colorkey’ in images

                   Changes in version 2.1.26                        
  

BUG FIXES

• Fixed ‘print’ method for plots and images to respect updating plotting parameters via ‘…’ arguments

                   Changes in version 2.1.25                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Add ‘run’ argument to ‘pixels’ for ‘MSImagingExperiment’

• Add ‘run’ argument to ‘plot’ for ‘MSImagingExperiment’

BUG FIXES

• Fixed bug in ‘ylab’ with one-sided formulas in ‘plot’

• Relaxed errors for out-of-range m/z values in ‘features’

• Value range of ‘colorkey’ now obeys ‘zlim’ argument

• NULL values for plot limits no longer give errors

                   Changes in version 2.1.24                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Documented new ‘options(Cardinal.dark=FALSE)’ default

BUG FIXES

• Fixed linear subsetting of models using ‘[’’ for ‘SparseResultImagingExperiment’ objects

• Check length of ‘classControl’ in ‘segmentationTest’

                   Changes in version 2.1.23                        
  

NEW FEATURES

• Added ‘slice’ for slicing imaging datasets (as a data cube)

• Added ‘alpha.power’ argument for ‘image’ methods

SIGNIFICANT USER-VISIBLE CHANGES

• Added documentation for options() under ‘?Cardinal’

                   Changes in version 2.1.22                        
  

NEW FEATURES

• Added new ‘Cardinal 2: Statistical methods’ vignette

                   Changes in version 2.1.21                        
  

NEW FEATURES

• Added ‘image3D’ methods for new classes

                   Changes in version 2.1.20                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Updated documentation and simulation examples

BUG FIXES

• Fixed bug in ‘summary’ for ‘SpatialShrunkenCentroids2’

                   Changes in version 2.1.19                        
  

NEW FEATURES

• Added ‘colocalized’ method for colocalization

• Added ‘colocalized’ method for colocalization

                   Changes in version 2.1.18                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Updated ‘Cardinal 2: User guide’ vignette

BUG FIXES

• Fixed bug in ‘simulateSpectrum’ when n > 1

                   Changes in version 2.1.17                        
  

NEW FEATURES

• Added ‘topFeatures’ method for extracting top-ranked features from statistical analyses

• Added ‘summary’ methods for new results objects

• Added ‘SummaryDataFrame’ for printing result summaries

SIGNIFICANT USER-VISIBLE CHANGES

• Deprecated ‘topLabels’ method -> use ‘topFeatures’

                   Changes in version 2.1.16                        
  

NEW FEATURES

• Added dplyr verbs for ‘DataFrame’ and “XDataFrame’

                   Changes in version 2.1.15                        
  

NEW FEATURES

• Added new ‘PCA’ method for ‘SparseImagingExperiment’

• Added new ‘PLS’ method for ‘SparseImagingExperiment’

• Added new ‘OPLS’ method for ‘SparseImagingExperiment’

SIGNIFICANT USER-VISIBLE CHANGES

• The ‘selectROI’ method will now use the last plot if no additional plotting arguments are given

• Setting ‘resolution’ on ‘MSProcessedImagingExperiment’ will now update the m/z values binning scheme

• The ‘select’ and ‘filter’ methods now using integers as row/col IDs without the ‘.id’ argument

BUG FIXES

• Fixed bug in ‘OPLS’ methods causing cross-validation to produce slightly optimistic results

                   Changes in version 2.1.14                        
  

NEW FEATURES

• New ‘mzAlign’ processing method for spectral alignment

• New ‘mzBin’ processing method for spectral binning

• New ‘crossValidate’ method that cleans up ‘cvApply’ output

• New normalization methods: ‘rms’ and ‘reference’

• New baseline reduction method: ‘locmin’

• New peak picking method: ‘mad’

• New ‘darkmode’ and ‘lightmode’ plotting options

• Added ‘cvApply’ methods for new classes

SIGNIFICANT USER-VISIBLE CHANGES

• Image plotting now uses different ‘colorkey’ legend placed beside plot that no longer obscures the image

• All plotting now uses different ‘strip’ labels placed above plot that no longer obscures the plot area

• All plotting now accept hidden ‘dark=TRUE’ argument to switch to plotting in new “dark mode”

• Changed/updated presets for ‘presetImageDef’ which provides presets for ‘simulateImage’ function

                   Changes in version 2.1.13                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Added message when printing a ‘SparseImagingExperiment’ object without un-applied pre-processing steps

BUG FIXES

• Added C routine registration with “C_” prefix for .Call

• Cleaned up ‘.o’ objects in /src created by accident

                   Changes in version 2.1.12                        
  

NEW FEATURES

• Added ‘meansTest’ method for linear model-based hypothesis tests of mean-summarized images

• Added ‘segmentationTest’ method for linear model-based hypothesis tests of spatially-segmented images

                   Changes in version 2.1.11                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Added option to set the probability regularization parameter (p0) to ‘spatialDGMM’ method

• Added option to initialize ‘spatialDGMM’ algorithm with either k-means or Gaussian mixture model

                   Changes in version 2.1.10                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Changed default colorscale for images to ‘viridis’

• Updated ‘simulateImage’ presets to handle multiple runs

                    Changes in version 2.1.9                        
  

NEW FEATURES

• Added ‘spatialDGMM’ method for fitting feature-wise spatially-aware Dirichlet Gaussian mixture models

• Added ‘predict’ method for ‘SpatialShrunkenCentroids2’

BUG FIXES

• Fixed ‘spatialShrunkenCentroids’ classification methods for new (‘SparseImagingExperiment’-based) classes

• Cleaned up unit tests for statistical methods

                    Changes in version 2.1.8                        
  

BUG FIXES

• Updated ‘PositionDataFrame’ initialization due to change in S4Vectors [<-,DataFrame behavior

• Updated ‘MassDataFrame’ initialization due to change in S4Vectors [<-,DataFrame behavior

                    Changes in version 2.1.7                        
  

BUG FIXES

• Updated ‘filter’ signature due to dplyr changes

                    Changes in version 2.1.6                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Added ImmunoOncology biocViews term

             Changes in version 2.1.5 (2018-12-14)                  
  

BUG FIXES

• Updated read/write methods for ‘matter’ filemode changes

             Changes in version 2.1.4 (2018-12-12)                  
  

SIGNIFICANT USER-VISIBLE CHANGES

• In ‘readImzML’ and ‘readAnalyze’, changed defaults from ‘attach.only=FALSE’ to ‘attach.only=TRUE’

• In ‘readImzML’ and ‘readAnalyze’, changed defaults from ‘as=MSImageSet’ to ‘as=MSImagingExperiment’

BUG FIXES

• Subsetting large ‘SparseImagingExperiment’ objects with ‘sparse_mat’ imageData should no longer hang

             Changes in version 2.1.3 (2018-12-12)                  
  

NEW FEATURES

• Added ‘ResultImagingExperiment’ class for results of statistical analyses of imaging experiments

• Added ‘spatialFastmap’ method for ‘SparseImagingExperiment’

• Updated ‘summarize’ to accept a ‘.group_by’ argument

• Added ‘simulateSpectrum’ and ‘simulateImage’ functions

SIGNIFICANT USER-VISIBLE CHANGES

• Automatically detect and setup ‘layout’ for new classes

• Using ‘layout’ now assumes (row, column) order when creating facet plots for new classes (only)

• Updated examples in documentation to use new classes

BUG FIXES

• Fixed bug in ‘spatialKMeans’ that caused ‘spatialFastmap’ to fail for datasets with fewer features than components

• Fixed bug where ‘plot’ did not facet over runs of a ‘SparseImagingExperiment’ when using ‘plusminus’

             Changes in version 2.1.2 (2018-11-30)                  
  

SIGNIFICANT USER-VISIBLE CHANGES

• Updated ‘spatialKMeans’ to use new ‘spatialFastmap’

• Updated ‘spatialShrunkenCentroids’ to use new spatially-aware discriminant scores calculation

             Changes in version 2.1.1 (2018-11-30)                  
  

NEW FEATURES

• Added ‘spatialFastmap’ method for performing spatially-aware FastMap projection more easily

             Changes in version 2.0.2 (2018-11-30)                  
  

BUG FIXES

• Fixed bug in ‘reduceDimension.peaks’ that caused peak intensities to be binned incorrectly

             Changes in version 2.0.1 (2018-11-14)                  
  

SIGNIFICANT USER-VISIBLE CHANGES

• Updated ‘peakFilter’ to check for freq.min >= 1 to accomodate old behavior (counts)

cbaf

             Changes in version 1.6.0 (2019-04-28)                  

New Features

• heatmapOutput now uses a more accurate algorithm for determining the margins.

• Terms updates. Package can recongize more cancers!

celaref

                   Changes in version 1.1.10                        

UPDATES

• Support for passing hdf5-backed SummarizedExperiment objects (internal conversion to sparse)

• Explicitly handle multiple assay() in the summarizedExperiment. Must have a named ‘counts’ assay, or, just the one unnamed assay.

BUG FIXES

• Subsampling per group should actually be used now.

                    Changes in version 1.1.8                        
  

UPDATES

• Updated vignette with large data handling.

• Doco updates

• make_ranking_violin_plot can pass parameters (e.g. rankmetrics) with …

                    Changes in version 1.1.4                        
  

UPDATES

• Methods/options to subset large datatsets.

                    Changes in version 1.1.3                        
  

UPDATES

• None. Version bump for build only.

                    Changes in version 1.1.2                        
  

UPDATES

• Testing tests

                    Changes in version 1.1.1                        
  

BUG FIXES

• Internal SingleCellAssay coercion bugfix. Should no longer require library(MAST) call to work.

UPDATES

• Partying hard with unit tests woo

                    Changes in version 1.1.0                        
  

UPDATES

• Option to change the gene ranking metric. Maybe useful for similar cell types like PBMCs.

• Use sparse matricies to support larger datasets in less RAM.

                    Changes in version 1.0.1                        
  

UPDATES

• First bioconductor version

celda

            Changes in version 0.99.34 (2019-04-23)                 

• Minor changes to the vignettes

            Changes in version 0.99.23 (2019-04-10)                 
  

• Remove pheatmap import

            Changes in version 0.99.22 (2019-04-09)                 
  

• Package celda, for bi-clustering of single-cell ‘omics data.

             Changes in version 0.99.8 (2019-03-11)                 
  

• Second submission to Bioconductor

             Changes in version 0.99.0 (2018-05-15)                 
  

• First submission to Bioconductor

CellBench

                   Changes in version 0.99.10                       

• Accepted into Bioconductor

New Features

• Added new vignettes for Tidyverse Patters and Method Wrappers

Modifications

• fn_arg_seq() now has a .strict argument to check if arguments supplied are actually used in the function. Default is FALSE, previously this check is always done, but it failed for functions that use methods dispatch. - pipeline_collapse() now has a data.name argument for if the name of the dataset should be kept in the pipeline string. Useful if only one dataset is used. - arrow_sep() now uses ascii glyphs (only left and right available) instead of unicode. Unicode arrows fail when ggplots in rmarkdown is compiled into PDF, a common enough use-case for this to be concerning.

                    Changes in version 0.0.7                        
  

Modifications

• purrr version number requirement set to (>= 0.3.0) because of argument name change in partial() - Documentation reorganised to clean up package documentation index. - Added landing page for ?CellBench

                    Changes in version 0.0.6                        
  

New Features

• Added propagation for errors - Added task_error class for errors - Added print method for task_error objects

                    Changes in version 0.0.5                        
  

New Features

• Added “Timing” vignette to explain time_methods - Changed apply_methods() to continue on errors and return error object in result column

                    Changes in version 0.0.4                        
  

Breaking Changes

• Changed .name arguments in time_methods() and apply_methods() to name

New Features

• Added time_methods function - Added set_cellbench_bpparam for more advanced parallelism options

                    Changes in version 0.0.3                        
  

New Features

• Implemented parallel application of methods to benchmark_tbl, previously only worked for dataset lists - Added fn_list constructor

• Added data_list constructor

                    Changes in version 0.0.2                        
  

Bug Fixes

• Fixed bug in apply_methods() causing it to fail when more than 1 thread is used

Modifications

• Updated introduction vignette to describe multithreading and function caching

                    Changes in version 0.0.1                        
  

• Minimal functioning package created - Compliant with BiocCheck::BiocCheck() and goodpractice::goodpractice()

CellMixS

                   Changes in version 0.99.9                        

• Prepared Bioconductor submission

ChAMP

                   Changes in version 2.13.2                        

• Changed ebayesGSEA function with a new name as ebGSEA, and added KPMT function in it.

CHETAH

             Changes in version 0.99.0 (2019-02-28)                 

• Submitted to Bioconductor

ChIPanalyser

                    Changes in version 1.4.1                        

Package Updates

• Updated Plotting functions

• Model quality assessment has been improved

• Noise Filter method for ChIP-seq Pre-processing

ChIPpeakAnno

                   Changes in version 3.17.2                        

• fix a bug in toGRanges to accept GTF files.

                   Changes in version 3.17.1                        
  

• fix the bug in annotatePeakInBatch which can not accept bindingType parameter.

ChIPseeker

                   Changes in version 1.19.1                        

• add origin_label = “TSS” parameter to plotAvgProf (2018-12-12, Wed)
• https://github.com/GuangchuangYu/ChIPseeker/issues/91

chromstaR

                    Changes in version 1.9.2                        

BUGFIXES

• Bugfix for error when exporting empty peak lists.

CHRONOS

                   Changes in version 1.11.1                        

• Replaced RBGL::brandes.betweenness.centrality() in pathwayMeasures() with igraph::betweenness() since the former is no longer available.

cleaver

             Changes in version 1.21.4 (2018-12-26)                 

• Use “https” in hyperlinks (where possible).

             Changes in version 1.21.3 (2018-12-26)                 
  

• Correct cleavage rules for “pepsin” and “pepsin1.3”. According to the peptidecutter documentation “pepsin1.3” is more specific (cleaves at [FL]) than “pepsin” (cleaves [FLWY]); see https://github.com/sgibb/cleaver/issues/6 for details. Thanks to Jean Manguy jean@manguy.eu for reporting this error.

             Changes in version 1.21.2 (2018-11-03)                 
  

• Convert vignette from Sweave to rmarkdown.

• Another try to fix links in manual pages to avoid WARNING on Windows.

             Changes in version 1.21.1 (2018-11-01)                 
  

• Add my ORCID to the Author field in DESCRIPTION.

• Fix links in manual pages to avoid WARNING on Windows.

CluMSID

                   Changes in version 0.99.13                       

• changed download instructions to BiocManager::install()

                   Changes in version 0.99.12                       
  

• Bioconductor review II: R, part three

• added MS2spectrum methods for MSnbase/ProtGenerics generics

• minor code changes with no visible effect for users

                   Changes in version 0.99.11                       
  

• fixed bug in new distanceMatrix(), now coerces numeric IDs to character

                   Changes in version 0.99.10                       
  

• Bioconductor review II: R, part two

• replaced nested for-loop inside distanceMatrix()

                   Changes in version 0.99.9                        
  

• Bioconductor review II: R, part one

• provided all ‘type’ argument options as vector

• added ‘…’ argument to specplot()

• changed function to convert MSnbase objects from ‘convertSpectrum(x)’ to ‘as.MS2spectrum(x)’ / ‘as(x, “MS2spectrum”)’

• various minor code changes with no visible effect for users

                   Changes in version 0.99.8                        
  

• Bioconductor review I: DESCRIPTION and NAMESPACE

• added URL and BugReports to DESCRIPTION

• started importing all packages into NAMESPACE

• abandoned “CluMSID_” prefix and renamed respective functions

• changed all function names to camel case starting with lower case letters

                   Changes in version 0.99.7                        
  

• further reduced size of vignettes

                   Changes in version 0.99.6                        
  

• bugfix in MTBLS vignette

                   Changes in version 0.99.5                        
  

• modified data import for CluMSID MTBLS vignette

                   Changes in version 0.99.4                        
  

• reduced size of vignettes

                   Changes in version 0.99.3                        
  

• added missing dependency for is()

                   Changes in version 0.99.2                        
  

• started avoiding class() function to check for class

• minor code style change

                   Changes in version 0.99.1                        
  

• removed .RHistory

• changed import for “show”

• removed invalid character from GC_post.csv in CluMSIDdata which caused errors on Linux and OS X

                   Changes in version 0.99.0                        
  

• Bioconductor submission

                   Changes in version 0.1.14                        
  

• deleted inst/extdata (now in CluMSIDdata)

                   Changes in version 0.1.13                        
  

• updated R version dependency to 3.6

• code style changes

                   Changes in version 0.1.12                        
  

• updated vignette dependencies

                   Changes in version 0.1.11                        
  

• added missing Suggests

• updated documentation and GC-EI-MS vignette

                   Changes in version 0.1.10                        
  

• added splitPolarities() function

• added specplot() function

                    Changes in version 0.1.9                        
  

• Featurelist() and writeFeaturelist() now also work with lists of ‘pseudospectrum’ objects

• bugfix for intensity extraction in extractPseudospectra()

• tutorial update

                    Changes in version 0.1.8                        
  

• added “…” to CluMSID_MDSplot(), CluMSID_HCplot(), CluMSID_OPTICSplot() to allow for customisation of plot appearance

                    Changes in version 0.1.7                        
  

• added polarity slot to ‘MS2spectrum’ class and respective show() generic

• added polarity accessor

• added extraction of polarity information from raw data to extractMS2spectra()

                    Changes in version 0.1.6                        
  

• added a NEWS file

• added “tolerance” argument for m/z tolerance to cossim() and distanceMatrix()

• added accessor functions for “MS2spectrum” and “pseudospectrum” objects

• added runnable examples for all exported functions

• some formatting and style changes

clusterProfiler

                   Changes in version 3.11.1                        

• asis parameter in [.compareClusterResult (2018-12-24, Mon) - https://github.com/GuangchuangYu/enrichplot/issues/17

CNVPanelizer

                   Changes in version 1.15.1                        

• Fix test due to change of sample function

CNVRanger

                    Changes in version 1.0.0                        

• Initial release of the ‘CNVRanger’ package

cola

                   Changes in version 0.99.15                       

• support t-SNE and UMAP.

                   Changes in version 0.99.14                       
  

• cola_report() supports mc.cores

                   Changes in version 0.99.13                       
  

• partition functions all support mc.cores

                   Changes in version 0.99.12                       
  

• implement get_consensus_matrix() by C++

• add regiester_NMF() and register_SOM()

                   Changes in version 0.99.9                        
  

• move TEMPLATE_DIR to .onLoad().

                   Changes in version 0.99.5                        
  

• reduce the number of packages loaded

• improve the package according to comments in https://github.com/Bioconductor/Contributions/issues/941#issuecomment-452728439

                   Changes in version 0.99.4                        
  

• fixed warnings in Rd files

                   Changes in version 0.99.3                        
  

• remove venneuler from DESCRIPTION

                   Changes in version 0.99.0                        
  

• Submitted to Bioconductor

coMET

             Changes in version 1.15.2 (2018-12-24)                 

• Update vignette (add warning=False)

             Changes in version 1.15.1 (2018-12-24)                 
  

• Update script to snp_ensembL

ComplexHeatmap

                   Changes in version 1.99.8                        

• add title_gap in `Legend()

• fixed a bug of wrong row title spaces when multiple heatmaps are vertically concatenated.

• fixed a bug of *_sub_title_side when the heatmap annotation is the first/last element in the heatmap list.

• zero-column/row heatmap is supported.

• improved calculation of axis breaks

                   Changes in version 1.99.7                        
  

• UpSet() supports adding complement sets.

• make_comb_set(): add universal_set and complement_size arguments.

• axes can be reversed in anno_* functions.

                   Changes in version 1.99.6                        
  

• adjust the size of heatmap annotations and add testing scripts.

• run multiple times k-means to get a consensus partition.

• show_heatmap_legend is set to FALSE if rect_gp = gpar(type = "none").

• add restore_matrix().

• add row_names_centered/column_names_centered arguments to Heatmap().

• gp in anno_text() supports fill and border.

• Legend adds boxplot-style legend.

• adjustment according to annotation extension is improved.

                   Changes in version 1.99.5                        
  

• add UpSet() and some related functions to make Upset plots

• fixed bugs of drawing legends

• add test_alter_fun()

• HeatmapAnnotation(): fixed a bug for setting height when all annotations are simple annotations.

• default_col(): if the fraction of positive values in the matrix is in (0.3, 0.7), the color mapping is symmetric to zero.

• check NA values in anno_boxplot() and anno_density().

• add mc.cores in densityHeatmap().

                   Changes in version 1.99.4                        
  

• anno_mark() is now calculated in multiple slices.

• oncoPrint(): automatically split the alteration type if the separator is one of “;:,|”.

• add anno_zoom()

                   Changes in version 1.99.1                        
  

• add cluster_row_slices and cluster_column_slices arguments in Heatmap().

• fixed a bug when annotation_height with only one annotation

• order of k-means slices are reordered by slice mean of row_reorder/column_reorder if they are provided as vectors.

• remove rsvg from Suggests.

                   Changes in version 1.99.0                        
  

This a major update of the package. The main changes are

• support column split

• support align heatmaps vertically

• add a naive AnnotationFunction class to handle annotation functions

• add more annotation functions

consensusDE

             Changes in version 1.0.7 (2019-03-01)                  

• export RUV corrected summarized file before model fit

• option to summarize read by transcript, exon or cds added to buildSummarized

• added chromosome coordinates to annotation of merged results

• include gtf or txdb as meta-data in summarized object

• added option, htseq_dir, to import HTSEQ count files to buildSummarized

• fixed sample_table format check (refactorise)

             Changes in version 1.0.6 (2019-12-31)                  
  

• add legend and label option to multi_de_plots

• fixing bug for paired mode model matrix in multi_de_pairs without RUV

• update vignette

             Changes in version 1.0.5 (2019-12-16)                  
  

• fixing first column name when writing tables for edgeR, Voom and DEseq

• fixed RUV model coefficients carrying through

             Changes in version 1.0.4 (2019-12-12)                  
  

• fixed ranking bug for combined data

• adding min_p to merged tables

             Changes in version 1.0.3 (2019-12-10)                  
  

• fixed ensembl_annotate option for multi_de_pairs

• added BiocGenerics as depends

             Changes in version 1.0.2 (2019-12-09)                  
  

• filter error update to buildSummarized

• add error reporting with incorrect pairs or group numbers

• add option to force_build to buildSummarized

• fix color bug in diag_plots

• fix annotation documentation for multi_de_pairs

• update filter option to permit from summarized experiment

• update vignette

             Changes in version 1.0.1 (2019-12-07)                  
  

• Fixed bugs - build gtf from path

coRdon

                    Changes in version 1.1.3                        

• Implemented codonTable subsetting with “[” and “[[”.

• Bug fix: ensured validity of codonTable when KEGG/COG annotations for some of the DNA sequences are missing.

CoRegFlux

             Changes in version 0.99.0 (2019-01-15)                 

• Submitted to Bioconductor

csaw

                   Changes in version 1.18.0                        

• Deprecated the type= argument in normOffsets().

• Removed the deprecated consolidateSizes() function.

• Deprecated the use of BPPARAM= in readParam(). Added the BPPARAM= argument to all relevant functions.

• Modified csawUsersGuide() to point to the workflow package.

cTRAP

                    Changes in version 1.0.3                        

• Add tag ImmunoOncology to BiocViews

                    Changes in version 1.0.2                        
  

• Fix comparison against CMap perturbations using gene set enrichment analysis (the resulting score was the additive inverse of the real scores)

                    Changes in version 1.0.1                        
  

• Update title, author names, version and README - Remove biomaRt dependency - By default, getL1000conditions now shows CMap perturbation types except for controls - Compare against CMap perturbations (compareAgainstL1000 function): - Remove “_t” from resulting column names (as the t-statistic may or may not be used) - Select p-value adjustment method when performing correlation analyses (Benjamini-Hochberg is set by default) - Documentation: - Fix obsolete function calls in function documentation - Hide non-exported functions from reference PDF manual

cydar

                    Changes in version 1.8.0                        

• Modified the plotSphere*() functions for more flexibility in colour choice.

• Added fix.zero= option in normalizeBatch() for range-based normalization.

cytofast

                   Changes in version 0.99.0                        

• Submitted to Bioconductor (in development)

dagLogo

                   Changes in version 1.21.4                        

• Fix the bug if there are multiple position in one peptides for fetchSequence.

                   Changes in version 1.21.3                        
  

• Update to grImport2

                   Changes in version 1.21.2                        
  

• merge the change by Haibo.

                   Changes in version 1.21.1                        
  

• documentation generated by RoxygenNote.

• add function cleanPeptides.

dcanr

             Changes in version 0.99.0 (2019-03-25)                 

• Submitted to Bioconductor

debrowser

                   Changes in version 1.10.7                        

• Better error reporting in data upload

• Better error reporting condition selection using metadata

• alldetected genes matrix downlad fixed in QC section

                   Changes in version 1.10.1                        
  

• LRT made default in DESeq2.

• Labels in main plots changed.

deco

                   Changes in version 0.99.53                       

• Bug fixes.

                   Changes in version 0.99.47                       
  

• Bug fixes.

• Annotation adapted to new “OrganismDbi” related packages.

• Three new diagnostic (plot) functions.

• Enlarged vignette.

                   Changes in version 0.99.42                       
  

• Bug fixes.

• Vignette converted into HTML format.

• Accepted in Bioconductor.

                   Changes in version 0.99.0                        
  

• Submitted to Bioconductor.

decompTumor2Sig

             Changes in version 1.99.1 (2019-04-07)                 

• Changed the procedure which converts lists of individual mutations from MPF files into tumor mutation profiles to reduce the memory footprint and allow for larger sets of tumors to be read from file.

• When genomes are read from files: remove genomes without SNVs (no mutation frequencies)

• Recognize indels for which either the REF or ALT base is specified as “-“

• Fix bugs: o Error when quadprog returned a mutation frequency of minimally larger than 1 (which is theoretically impossible but can probably happen due to the rounding of floating point numbers)

             Changes in version 1.99.0 (2018-11-10)                 
  

• When transcription direction is taken into account: exclude mutations in regions with overlapping genes of opposing transcription directions by default! Previous versions of decompTumor2Sig took the approach of pmsignature, using the transcription direction of the first gene encountered in the transcript database (which is rather arbitrary); excluding these mutations appears more appropriate. The old approach can still be used with an additional function parameter.

• Removed pmsignature from the suggested packages (not allowed in Bioconductor)

• Reduced the number of tumor genome examples in extdata for faster processing and smaller package size (six out of 21 tumors from PMID:22608084)

             Changes in version 1.3.3 (2018-09-24)                  
  

• Implemented own signature plotting to remove code dependency from pmsignature

• Decoupled the following data conversions functions from pmsignature code: o getGenomesFromMutFeatData() o getSignaturesFromEstParam()

• Moved some common code to a new internal function for ease of maintenance.

• Fixed bugs: o Error when some sequence names where not found in the reference genome, e.g., due to different names of decoy sequences. o Minor problems with unlikely signatures composed of only the mutated base (no flanking bases)

             Changes in version 1.3.2 (2018-08-29)                  
  

• Fixed a minor bug in mapSignatureSets() that occurred when the two signature sets had the same size.

• Added functions to verify the format of signatures, genomes and exposures: o isAlexandrovSet(), isShiraishiSet(), isSignatureSet() o sameSignatureFormat() o isExposureSet()

• Moved description of deprecated BiocInstaller in vignette to BiocManager.

             Changes in version 1.3.1 (2018-08-15)                  
  

• Updated DESCRIPTION file o replaced Author and Maintainer by Authors@R o added URL for BugReports

• Changed from manual NAMESPACE and *Rd files to a creation by roxygen2

• Changed function names for reading data from “load…” to “read…”

• Shortened the longest function names o getGenomesFromMutationFeatureData -> getGenomesFromMutFeatData o getSignatureListFromEstimatedParameters -> getSignaturesFromEstParam

• Used robust sequence creation with seq, seq_len, seq_along instead of 1:N etc

• Consistent use of native class checking such as is.numeric()

• Implemented wrapper functions for external classes which do not provide the necessary accessor functions

• Replaced instances of sapply() and unlist(lapply()) by vapply()

• Updated vignette and made most code chunks runnable

• Added greedy search option to plotExplainedVariance (significant speed-up)

             Changes in version 1.3.0 (2018-07-26)                  
  

• Submitted to Bioconductor

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”)

DEGreport

                   Changes in version 1.19.2                        

• Fix: Error when metadata doesn’t contain group column. Thanks to @hexaflexa.

• Fix: Update documentation link in degComb.

• Fix: Fix error when factor has extra-levels by @roryk.

• Fix: Fix cutoff summary in degPattern.

                   Changes in version 1.19.1                        
  

• Feature: Accept data.frame to plot custom clusters.

• Feature: Add cluster consistency plot to degPattern.

DelayedArray

                   Changes in version 0.10.0                        

NEW FEATURES

• Many improvements to matrix multiplication (%*%) of DelayedMatrix objects by Aaron Lun. Also add limited support for (t)crossprod methods.

• Add rowsum() and colsum() methods for DelayedMatrix objects. These methods are block-processed operations.

• Many improvements to the RleArray() contructor (see messages for commits 582234a7 and 0a36ee01 for more info).

• Add seedApply()

• Add multGrids() utility (still a work-in-progress, not documented yet)

DelayedMatrixStats

                    Changes in version 1.5.1                        

• Move rowsum() and colsum() to DelayedArray package. Thanks @hpages (https://github.com/PeteHaitch/DelayedMatrixStats/pull/56).

DeMixT

                   Changes in version 0.99.0                        

• New package DeMixT, for cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms

derfinder

                   Changes in version 1.17.3                        

NEW FEATURES

• Add ORCID’s following changes at http://bioconductor.org/developers/package-guidelines/#description

                   Changes in version 1.17.2                        
  

BUG FIXES

• Use R’s random seeds from version 3.5.0 for the test thanks to https://twitter.com/StrictlyStat/status/1103303028751372289

derfinderHelper

                   Changes in version 1.17.3                        

NEW FEATURES

• Add ORCID’s following changes at http://bioconductor.org/developers/package-guidelines/#description

                   Changes in version 1.17.2                        
  

BUG FIXES

• Use R’s random seeds from version 3.5.0 for the test thanks to https://twitter.com/StrictlyStat/status/1103303028751372289

derfinderPlot

                   Changes in version 1.17.2                        

NEW FEATURES

• Add ORCID’s following changes at http://bioconductor.org/developers/package-guidelines/#description

DEsubs

                    Changes in version 1.9.1                        

• Added biocViews tag.

diffcyt

                   Changes in version 1.3.17                        

• Add additional optional arguments for methods ‘testDA_edgeR’, ‘testDS_limma’, and ‘testDS_LMM’.

                   Changes in version 1.3.12                        
  

• Allow selecting columns of ‘experiment_info’ with character vector of column names, when creating design matrix or model formula.

                    Changes in version 1.3.6                        
  

• Renamed and extended summary table function ‘topTable’ (previously ‘topClusters’).

diffuStats

                    Changes in version 1.3.1                        

• Fixed vignette title and citation - Small changes to documentation
• Version number not malformed anymore

DiscoRhythm

             Changes in version 0.99.8 (2019-04-29)                 

• New URL for public server

             Changes in version 0.99.7 (2019-04-29)                 
  

• Write intermediate report files to same directory as output report

             Changes in version 0.99.6 (2019-04-26)                 
  

• Addition of ncores and port arguments to discoApp

             Changes in version 0.99.4 (2019-04-24)                 
  

• Addition of more unit tests on inputs

• Bug fixes

• Addition of more unit tests on inputs

• Bug fixes

             Changes in version 0.99.3 (2019-04-18)                 
  

• Bug fixes

             Changes in version 0.99.2 (2019-04-18)                 
  

• Use match.arg for argument options

             Changes in version 0.99.1 (2019-04-09)                 
  

• Added support for usage of SummarizedExperiment objects

             Changes in version 0.99.0 (2019-04-04)                 
  

• Submitted to Bioconductor

dmrseq

             Changes in version 1.3.1 (2018-11-02)                  

• dmrseq now requires that input BSseq objects be ordered (as the BSseq() constructor no longer automatically orders loci).

DNABarcodeCompatibility

             Changes in version 0.99.8 (2018-11-25)                 

• Notify that the package was approved by Bioconductor

• Fixed all Bioconductor reviewer’s comments and updated documentation section accordingly. Passed BioCheck 1.18 locally

             Changes in version 0.99.7 (2018-11-19)                 
  

• Updated documentation section. Passed BioCheck 1.18 locally

             Changes in version 0.99.6 (2018-11-19)                 
  

• Change installation procedure to allow package install on R<3.6. Passed BioCheck 1.18 locally

             Changes in version 0.99.5 (2018-11-19)                 
  

• Remote BiocCheck imposes R >=3.6. Passed BioCheck 1.18 locally

             Changes in version 0.99.4 (2018-11-19)                 
  

• Improved error handling. Passed BioCheck 1.18 locally

             Changes in version 0.99.3 (2018-11-13)                 
  

• Fixed R version to 3.5. Passed BioCheck 1.18 locally

             Changes in version 0.99.2 (2018-11-13)                 
  

• New package features for the Shiny interface. Passed BioCheck 1.18 locally

             Changes in version 0.99.1 (2018-10-15)                 
  

• Passed BioCheck 1.17 locally

             Changes in version 0.99.0 (2018-10-15)                 
  

• Prepared package for submission to Bioconductor repository (BioCheck 1.16)

DominoEffect

                    Changes in version 1.3.1                        

UDPATE

• change Ensembl version from 73 to 75

                    Changes in version 1.3.0                        
  

NEW FEATURES

• DominoEffect in BioC 3.9 development release

DOSE

                    Changes in version 3.9.4                        

• export parse_ratio (2019-03-29, Tue)

• bug fixed of get_enriched (2019-01-14, Mon) - https://github.com/GuangchuangYu/clusterProfiler/issues/177

                    Changes in version 3.9.2                        
  

• mv enrichment vignettes to clusterProfiler-book (2019-01-10, Thu)

                    Changes in version 3.9.1                        
  

• asis parameter in [.enrichResult and [.gseaResult (2018-12-24, Mon)
• https://github.com/GuangchuangYu/enrichplot/issues/17

doseR

                   Changes in version 0.99.5                        

• Resolved biocCheck errors, warnings and notes.

• Completed SummarizedExperiment integration.

DropletUtils

                    Changes in version 1.4.0                        

• Removed read10xMatrix().

• Supported CellRanger v3 output files in read10xMolInfo(), read10xCounts(), write10xCounts().

• Modified barcodeRanks() to return a DataFrame with knee/inflection estimates in metadata.

• Slight change to random number generation in emptyDrops() to be agnostic to number of cores.

easyRNASeq

                   Changes in version 2.19.6                        

• More fiddling with documentation link warnings on windows

                   Changes in version 2.19.5                        
  

• Fixed more documentation link warnings on windows

                   Changes in version 2.19.4                        
  

• Fixed link warnings on windows

                   Changes in version 2.19.3                        
  

• Changed to use BiocFileCache for the tests and examples

                   Changes in version 2.19.2                        
  

• Added the volume and page in the citation

• Added the ImmunoOncology field per request from Bioc core

• Fixed the documentation warnings on Windows

                   Changes in version 2.19.1                        
  

• Dropped the RangedData support as these are now deprecated.

                   Changes in version 2.18.4                        
  

• Changed from curl_download to download.file

• Bioc core changes

                   Changes in version 2.18.2                        
  

• Added the ImmunoOncology field per request from Bioc core

• Added the volume and page in the citation

• Fixed the documentation warnings on Windows

                   Changes in version 2.18.1                        
  

• Adapted an example as RangedData objects are being deprecated.

edgeR

                   Changes in version 3.26.0                        

• read10X() now automatically detects files names from latest CellRanger version.

• glmTreat() now checks whether ‘contrast’ is a matrix with multiple columns and uses first column.

• The TMMwzp method has been renamed to TMMwsp, but calls to method=”TMMwzp” will still be respected. calcNormFactors(object) now returns a named vector when ‘object’ is a matrix, with colnames(objects) as the names.

• New ‘random’ method for zscoreNBinom().

• Add arguments ‘log’ and ‘prior.count’ to cpmByGroup() and rpkmByGroup().

• Bug fix to filterByExpr().

ENCODExplorer

                    Changes in version 2.9.0                        

NEW FEATURES

• The ENCODExplorer was split into 2 packages: ENCODExplorer and ENCODExplorerData

• The encode_df object is now available through the AnnotationHub

• The functions to interact with the ENCODExplorer API (except the search function) were moved to the ENCODExplorerData

EnhancedVolcano

                    Changes in version 1.1.4                        

• changed ‘colOverride’ to ‘colCustom’

• added a new ‘shape’ parameter to control the shape of plotted points

• added a new ‘shapeCustom’ parameter, akin to functionality supplied by ‘colCustom’ (formerly ‘colOverride’)

• added functionality to add title, subtitle, and caption (parameters: title, subtitle, caption, titleLabSize, subtitleLabSize, captionLabSize = 12)

• added functionality to add extra vertical and horizontal lines (parameters: hline, hlineType, hlineCol, hlineWidth, vline, vlineType, vlineCol, vlineWidth)

• changed ‘colConnectors’ default from “black” to “grey10”

• added extra parameters for line connectors (parameters: typeConnectors, endsConnectors, lengthConnectors)

• ‘labhjust’ and ‘labvjust’ are now ‘transcriptLabhjust’ and ‘transcriptLabvjust’, respectively

• user can now specify to draw transcript labels as text and text in boxes via ‘boxedlabels’ (TRUE/FALSE)

                    Changes in version 1.1.2                        
  

• added functionality to shade specific genes in the plot space (parameters: shade, shadeLabel, shadeAlpha, shadeFill, shadeSize, shadeBins)

• added new parameters ‘labhjust’ and ‘labvjust’ for fine tuning position of labels

• suppress warnings about removal of missing values

• now easier to hide the legend via legendVisible = TRUE/FALSE

EnrichedHeatmap

                   Changes in version 1.13.1                        

• update the package according to the new version of ComplexHeatmap (>= 1.99.0)

• removed EnrichedHeatmap class and now the enriched heatmap is purely a Heatmap class object.

• add flip_upstream argument in normalizeToMatrix().

• pos_line and pos_line_gp use the setting in EnrichedHeatmap() by default.

• colSds -> matrixStats::colSds

enrichplot

                    Changes in version 1.3.2                        

• dotplot supports setting x to other variable, e.g. NES (2019-01-10, Thu) - mv vignette to clusterProfiler-book.

enrichTF

             Changes in version 1.0.0 (2019-04-30)                  

• Transcription factors enriched in regions based on Bioconductor is released.

• Initial release version contains pipeline and all dependents for transcription factors enrichment analysis in given regions. User only need to provide a BED file and can obtain significant enriched transcription factors’ p-values of three statistic test.

             Changes in version 0.99.0 (2019-03-21)                 
  

• Submitted to Bioconductor

ensembldb

                   Changes in version 2.7.10                        

• Export getGenomeTwoBitFile (issue #95).

• Update vignette on using getGenomeTwoBitFile instead of getGenomeFaFile.

                    Changes in version 2.7.9                        
  

• Add intronsByTranscript method (issue #94).

                    Changes in version 2.7.7                        
  

• Performance improvement for proteinToTranscript.

                    Changes in version 2.7.6                        
  

• Increase performance of genomeToTranscript for input GRanges of length > 1.

                    Changes in version 2.7.5                        
  

• Fix class definitions for R >= 3.6.

                    Changes in version 2.7.4                        
  

• Update perl script to add columns tx_id_version and gene_id_version to the transcript and gene database tables.

                    Changes in version 2.7.3                        
  

• Implement mapIds multiVals = “CharacterList” option (issue #87).

                    Changes in version 2.7.2                        
  

• Add vignette with coordinate mapping use cases

                    Changes in version 2.7.1                        
  

• transcriptToGenome returns an empty GRanges if the input range is outside of the transcript’s sequence instead of throwing an error.

ensemblVEP

                   Changes in version 1.26.0                        

• add support for Ensembl release 95/96

EpiDISH

                    Changes in version 2.0.0                        

• Add CellDMC and hepidish functions.

epihet

                   Changes in version 0.99.0                        

IMPROVEMENTS AND BUG FIXES

• updates for review

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>

evaluomeR

            Changes in version 0.99.81 (2019-02-26)                 

• Updated DESCRIPTION metadata

             Changes in version 0.99.8 (2019-02-19)                 
  

• Removed dependency with orphaned ‘fpc’ CRAN package

             Changes in version 0.99.7 (2019-02-19)                 
  

• The method ‘correlations’ is now ‘metricsCorrelations’

             Changes in version 0.99.6 (2019-02-19)                 
  

• Internal improvements according to Bioconductor reviews

             Changes in version 0.99.5 (2019-02-19)                 
  

• Removing some @examples so that they do not exceed the time limit of Bioconductor check

             Changes in version 0.99.4 (2019-02-16)                 
  

• The correlations method also uses SummarizedExperiment as output object.

             Changes in version 0.99.3 (2019-02-16)                 
  

• All methods depend on SummarizedExperiment as input/output object.

             Changes in version 0.99.2 (2019-02-15)                 
  

• SummarizedExperiment can be now processed via seToDataFrame method. Adding SummarizedExperiment and airway dependencies.

             Changes in version 0.99.1 (2019-02-11)                 
  

• Submitted to Bioconductor

ExperimentHub

                    Changes in version 1.9.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• (1.9.2) The Hubs have been updated to use BiocFileCache as a backend utility for managing and downloading resources. This allows for file specific caching mechanism. This change is a significant user change as it changed the default directories for the Hubs (AnnotationHub/ExperimentHub) as well as the base directory no longer being hidden.

ExperimentHubData

                    Changes in version 1.9.0                        

NEW FEATURES

• Added ability to have multiple RDataPaths associated with single hub id for strongly associated files (like bam and its bai index file)

FamAgg

                   Changes in version 1.11.5                        

• Ensure same ordering of pedigree and provided labels in buildPed (issue #19).

                   Changes in version 1.11.4                        
  

• Fix bug in buildPed with prune = TRUE that resulted in either a missing mother or father in some complicated family structures.

                   Changes in version 1.11.3                        
  

• Fixed bug in buildPed missing out mates in some special cases.

• Fixed bug in buildPed causing differences between individual IDs and rownames of the pedigree data.frame.

                   Changes in version 1.11.2                        
  

• Fix corner case in generating plotting data pedigree.

• Add -family parameter for haplopainter, got lost during refactoring (issue #16 aftermath).

                   Changes in version 1.11.1                        
  

• Fix issue with ids in the pedigree being factors.

FELLA

                    Changes in version 1.3.1                        

• Fixed main vignette title to match that of paper

• Fixed Unicode char' (U+301) error (had a tilde as \'\i in bibfile)

• Added citation to BMC article

fgsea

                    Changes in version 1.9.6                        

• Fix in log2err calculation

• Small fixes for plotGseaTable

                    Changes in version 1.9.2                        
  

• Added fgseaMultilevel function for more accurate logPval estimation

fishpond

                   Changes in version 0.99.30                       

• added two interaction tests, described in ?swish

• incorporate qvalue package for pvalue, locfdr and qvalue

• added plotMASwish() to facilitate plotting

• wilcoxP is removed, and the mean is used instead

                   Changes in version 0.99.0                        
  

• fishpond getting ready for submission to Bioc

flowAI

                   Changes in version 1.12.5                        

• increased pen_valueFS default value

                   Changes in version 1.12.2                        
  

• fix bug with render function

flowCL

                   Changes in version 1.21.1                        

• Changed endpoint in man pages, and added ImmunoOncology as a biocViews tag.

                   Changes in version 1.21.0                        
  

• Same as previous. Bumped by BioConductor.

flowClust

                   Changes in version 3.21.2                        

• Fixed some tests and rewrote the vignette with Rmarkdown.

FoldGO

             Changes in version 1.1.2 (2019-04-12)                  

• Bug with missing set of background genes fixed

                    Changes in version 1.1.1                        
  

• Bug with p-value correction before filtering fixed

             Changes in version 1.1.0 (2018-10-31)                  
  

• First release

GAPGOM

             Changes in version 1.0.0 (2018-02-13)                  

Added

• Installation chapter to main vignette.

• Extra tests.

• Basic user input checks.

• Tests for checking precalculated matrices versions.

• Package added to Bioconductor

• Extra script for potential addition in the future (chromosome position calculations. File is in inst folder: “chrom_pos.R”)

Changed

• Interfacing with GO.db to increase performance (gets converted to environment first).

• The way TopoICSim is calculated for genes/genelists, skipping certain unnecessary calculations, improving performance greatly.

• apply functions.

• How test results are stored -> they are now stored in a list instead of seperately.

• Examples, tests and vignette calculations to make sure they don’t last too long.

• Readme, more verbose.

• Vignettes/Documentation - typo fixes and general small improvements.

Removed

• All global assignments.

• Class accessors (where possible).

Fixed

• “Fixed” news file to plain text format.

• Precalculated topoicsim matrix.

• Compliance with R CMD check.

• Compliance with R CMD BiocCheck.

• Dependency issues.

• Download function of fantom data.

• Fantom 5 functions.

• Calculation time output (actually in seconds now).

             Changes in version 0.3.0 (2018-11-22)                  
  

Added

• Re-added data which lncRNApred’s paper is based on.

• Support for all AnnotationDbi Key types.

• Vignette for GAPGOM.

• Vignette for benchmarks/performance measuring.

• Term algorithm as exported function.

• Set go data as exported function.

• Some frequently used params can now be set manually (go_data, All_Go_pairs).

• Seperate scoring function (If people want to do their own enrichment/only get semantic similarity scores).

• Some more arguments for the algorithms to make the user have more control.

• Custom gene interface for topoicsim.

Changed

• DESCRIPTION file, now adheres to some smaller requirements Bioconductor enforces.

• Data preparation functions, they are now updated and more clear.

• Topoicsim for gene and geneset are now 1 generic function topo_ic_sim_genes.

• Documentation and comments (again).

• Argument parsing for topoicsim.

• Some tests and their results.

• Used arguments in both algorithms.

• Precalculated values are deprecated for this version and thus turned off, warning gets shown if it is tried to be used anyway. The values will be updated in upcoming releases and probably adhere to only certain org.db package versions (with a warning shown if incorrect versions are used).

• Some lapply loops, now for loops, as they were using global assignments and this is forbidden/unfavorable in conventions.

• Updated data-raw files, they now work properly for current version and are better documented.

Removed

• All forms of parallelization support. It was buggy/inconsistent and where it could be implemented insignificant performance gains were made.

• Fantom5 example data

• Direct interface from fantom5 file to expset fantom_load_expressionset().

Fixed

• Inconsistent result of lncrnapred compared to original algorithm. Now is exactly the same.

• Documentation of internal functions is now hidden.

• data-raw missing in .Rbuildignore.

• R CMD check failing because of different lncRNApred results in factor indices. Fixed by converting unnecesary factors to chars.

• R CMD check failing because of T and F usage instead of TRUE/FALSE.

• fantom_to_expset() not always loading correctly; mouse and human had different metadata.

             Changes in version 0.2.0 (2018-10-20)                  
  

Added

• TopoICSim performance improvements.

• LncRNApred performance improvements.

• Parallelisation for combined method

• Some small extra options for similarity prediction.

• Precalculated similarity scores between frequent GO terms.

• Data preperation file, describing methods used for generating package data.

• Progress bars for TopoICSim.

• Basic tests (for main algorithms only).

• Some small tests for the main algorithms.

• LICENSE file.

Changed

• Return value of main TopoICSim between gene sets to better match return value of TopoICSim between two genes.

• All functions are now pre-compiled (except for data_gen.R).

• Imports (per function).

• Comments, a lot of them.

• Implementation of entrez -> goid lookup. (some ids get looked up twice)

• data.frame subsetting/ddply functions –> replaced with way faster data.table alternatives.

• Vectorisation of parts that weren’t yet vectorized.

• Changed some loops back to for loops instead of apply –> some weren’t a good use case for apply.

• Some matrixes now use the Matrix library.

Removed

• Nothing.

Fixed

• R depends version (3.4.4 –> 3.5.1).

• Performance bug in TopoICSim (#4).

• Performance bug in entrez -> goid lookup (#5).

• fdr bug (#7).

• Bug where id_select_vector was actually selected for rather than filtered for (#8).

• Topoicsim being a total memory hog, it left a lot of unused items in ram –> using gc() now as an optional argument.

• Newline loading bar bug (#9).

             Changes in version 0.1.0 (2018-10-04)                  
  

Added

• Changelog (NEWS.md).

• Better input interface and refactoring towards ExpressionSet based system.

• Replacement for current example data by ExpressionSet class of fantom5 annotated data (small subset of fantom5).

• Documentation file for previously mentioned new data.

• EntrezID based system for looking up GO ids instead of hardcoded translation table without source.

Changed

• Small refactor to switch case in expression_prediction_function().

• A lot of refactoring in expression_prediction_function() and enrichment_analysis() to make it work with ExpressionSets.

• Documentation of lncRNApred related functions

Removed

• Old example/expression data and their documentation, this will be re-added later once proper source is known.

Fixed

• Bumped up y version number to correct Bioconductor version conventions.

• Small typo in zzz.R

• .gitignore mistake (still including .Rdata temp files… These got really big :( )

• File typo data_preperation.R –> data_preparation.R

             Changes in version 0.0.1 (2018-09-25)                  
  

Added

• Expression metric prediction algorithm made by Rezvan Ehsani and Finn Drablos.

• TopoICSim algorithm/measure made by Rezvan Ehsani and Finn Drablos.

• Documentation to the previously denoted algorithms and metrics.

• Default datasets to compute some examples with.

GateFinder

                    Changes in version 1.3.2                        

• fixed conditional statement issue

                    Changes in version 1.3.0                        
  

• Bug fix re.removing unnecessary suggestion of flowUtils.

gdsfmt

                   Changes in version 1.20.0                        

UTILITIES

• optimize the C implementation of ‘packedreal8’ using a look-up table

NEW FEATURES

• new data types ‘packedreal8u’, ‘packedreal16u’, ‘packedreal24u’ and ‘packedreal32u’

BUG FIXES

• the compression method ‘LZ4_RA.max’ does not compress data

• add.gdsn() fails if a factor variable has no level

• add.gdsn(, storage=index.gdsn()) accepts the additional parameters from index.gdsn(), e.g., ‘offset’ and ‘scale’ for packedreal8

                   Changes in version 1.18.1                        
  

BUG FIXES

• the node name should not contain a slash ‘/’

GeneNetworkBuilder

                   Changes in version 1.25.1                        

• update author’s email.

GENESIS

                   Changes in version 2.13.7                        

• Remove all monomorphic variants (including all heterozygotes) from association test results.

                   Changes in version 2.13.3                        
  

• Restore option to run pcair without kinship matrix.

                   Changes in version 2.13.2                        
  

• Add option to use imputed dosage in association tests.

GENIE3

                    Changes in version 1.5.2                        

• Adding check for duplicated rownames (gene id/names)

• Bugfix in getLinkList: diag <- NA

GenomeInfoDb

                   Changes in version 1.20.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Update genomeMappingTbl.csv, the db used internally by genomeBuilds() and family.

BUG FIXES

• Fix bug in seqlevelsStyle() (see https://github.com/Bioconductor/GenomeInfoDb/issues/3 for more information)

• Fix fetchExtendedChromInfoFromUCSC(“hg38”), which got broken by a recent change on the UCSC side (see https://support.bioconductor.org/p/117808/#117831 for more information)

GenomicDataCommons

                    Changes in version 1.7.4                        

• slicing available for multiple regions

• added significant new query capabilities

• Simple Somatic Mutations (see ssms and ssm_occurrences)

• Copy Number Variations (see cnvs and cnv_occurrences)

• Gene details (see genes)

GenomicFeatures

                   Changes in version 1.36.0                        

NEW FEATURES

• Export and document helper functions tidyTranscripts(), tidyExons(), and tidyIntrons()

• Add support for mapToTranscripts() to map ranges that span introns

BUG FIXES

• Fix bug in makeTxDbFromGFF() when file is a GFF3File or GTFFile object

• Fix bug in makeFeatureDbFromUCSC() (see https://github.com/Bioconductor/GenomicFeatures/issues/15)

• Fix makeTxDbFromUCSC() on hg19/refGene and hg38/refGene tables (see message of commit ee575ee8 for more information)

GenomicRanges

                   Changes in version 1.36.0                        

NEW FEATURES

• findOverlaps() now supports type=”equal” on GRangesList objects

DEPRECATED AND DEFUNCT

• After being deprecated in BioC 3.8, the seqinfo() setter, seqnames(), and findOverlaps() are now defunct on RangedData objects.

GenomicScores

                    Changes in version 1.8.0                        

USER VISIBLE CHANGES

• Added support to latest release 2.1 of gnomAD MAF data lifted to GRCh38 by Ensembl, stored in packages MafDb.gnomAD.r2.1.GRCh38 and MafDb.gnomADex.r2.1.GRCh38.

BUG FIXES

• Bugfix in the support to TOPMED MAF data, to discard variants whose VCF FILTER is not set to PASS.

GEOquery

                   Changes in version 2.51.1                        

Improvements

• Add formal experimentData slot to GSE records. Of class MIAME. [from @vlakam]

ggtree

                   Changes in version 1.15.6                        

• remove getChild, getChild.df, getParent, getParent.df, getSibling, getAncestor and getAncestor.df, instead use child, parent, sibling and ancestor methods implemented in tidytree and treeio (2019-01-30, Wed) - remove get.offspring.df and get.offspring.tip and instead use tidytree::offspring (2019-01-28, Mon) - facet_widths function to set relative widths of facet panels (2019-01-28, Mon) - the output is ggplotify::as.ggplot(grid_object), so it is not the original ggtree object.

                   Changes in version 1.15.5                        
  

• bug fixed of theme_tree2 (2019-01-14, Mon) - https://github.com/GuangchuangYu/ggtree/issues/218 - mv rescale_tree to treeio (2019-01-11, Fri)

                   Changes in version 1.15.4                        
  

• reimplement MRCA as a method inherited from tidytree (2019-01-10, Thu) - mv vignettes to treedata-book

                   Changes in version 1.15.3                        
  

• move reroot method to treeio package and rename to root (2018-12-28, Fri) - bug fixed for setting branch.length=”none” in unrooted layouts (2018-12-26, Wed) - bug introduced in https://github.com/GuangchuangYu/ggtree/pull/201

                   Changes in version 1.15.2                        
  

• compatible with tibble v=2.0.0 (2018-11-29, Thu)

                   Changes in version 1.15.1                        
  

• now revts also reverse the branch column (2018-11-11, Sun) - https://groups.google.com/d/msgid/bioc-ggtree/50765a34-53e5-44d2-bb8f-6d20a11fa890%40googlegroups.com
• better msg when taxa name not consistent in sequence and tree files with msaplot. (2018-11-07, Wed) - https://github.com/GuangchuangYu/ggtree/issues/172#issuecomment-436585370

GladiaTOX

                   Changes in version 0.99.0                        

• Submitted to Bioconductor

GNET2

                   Changes in version 0.99.13                       

• Added heuristic split of regression trees by K-means.

                   Changes in version 0.99.6                        
  

• Improve the performance for module building with R code, now build_moduleR has same level of performance with its C++ version.

                   Changes in version 0.99.5                        
  

• Submitted to Bioconductor.

                   Changes in version 0.99.1                        
  

• Initial release.

GOfuncR

                    Changes in version 1.3.4                        

USER-LEVEL CHANGES

• update GO-graph to weekly release (version 27-Mar-2019)

• fix issue with “~” as abbreviation for home directory in custom ontology path

                    Changes in version 1.3.3                        
  

USER-LEVEL CHANGES

• update GO-graph (version 26-Mar-2019)

gpuMagic

             Changes in version 0.99.6 (2019-04-19)                 

• Add more function documentation

             Changes in version 0.99.5 (2019-04-18)                 
  

• Fix grammar issue

                   Changes in version 0.1.19                        
  

• Add “customized opencl code” vignette

                   Changes in version 0.1.16                        
  

• Implement memory pool

             Changes in version 0.1.7 (2019-02-15)                  
  

• Fix the incorrect local thread number

             Changes in version 0.1.3 (2019-02-15)                  
  

• Adding Mac builder flag

• Bugs fixing

             Changes in version 0.1.2 (2019-02-13)                  
  

• Trying to fix the build error

             Changes in version 0.1.1 (2019-02-13)                  
  

• Trying to fix the build error

             Changes in version 0.1.0 (2019-02-13)                  
  

• Submitted to Bioconductor

graper

             Changes in version 0.99.0 (2018-11-07)                 

• Submitted to Bioconductor

graphite

             Changes in version 1.29.3 (2019-04-17)                 

• Updated all pathway data.

gtrellis

                   Changes in version 1.15.2                        

• fixed warnings in Rd files.

                   Changes in version 1.15.1                        
  

• Use new definition of Legends-class.

Guitar

             Changes in version 1.99.0 (2019-04-24)                 

• The following changes have been made primarily in this release:

• 1. Add a confidence interval for the curve
• 1. Modify GuitarcoordinateTXDB to remove the generation of the bin interval of the guitar coordinate system.
• 1. Sampling the input site information file.
• 1. Change the coordinate structure and normalize the abscissa of the coordinate system to the interval 0~1.
• 1. Change the composition and calculation of weight in the density drawing method.
• 1. Open various parameters in the drawing process to the user for selection.

Gviz

                   Changes in version 1.28.0                        

BUG FIXES

• Fixed issue with hg19 genome version and BiomartGeneRegionTrack: user needs to provide biomart object pointing to grch37.ensembl.org

• Fixed IdeogramTrack to use user provided title

HCABrowser

                    Changes in version 1.0.0                        

• HCABrowser released

HDF5Array

                   Changes in version 1.12.0                        

NEW FEATURES

• Add ‘prefix’ arg to save/loadHDF5SummarizedExperiment()

• Add quickResaveHDF5SummarizedExperiment() for fast re-saving after initial saveHDF5SummarizedExperiment(). See ?quickResaveHDF5SummarizedExperiment for more information.

• Add h5mread() as a faster alternative to rhdf5::h5read(). It is now the workhorse behind the extract_array() method for HDF5ArraySeed objects. This change should significantly speed up block processing of HDF5ArraySeed-based DelayedArray objects (including HDF5Array objects).

HiCBricks

                    Changes in version 1.1.5                        

• HDF file locking option has been removed.

• data.table warning is now disabled while reading entire matrices.

• Vignette documentation has been converted to Rmd and BiocStyle html output.

HilbertCurve

                   Changes in version 1.13.3                        

• set interpolate = FALSE in grid.raster()

• improved hc_map()

                   Changes in version 1.13.2                        
  

• fixed warnings in Rd files

                   Changes in version 1.13.1                        
  

• update with new definition of legends

hipathia

             Changes in version 1.5.1 (2019-02-21)                  

• Adding function node_color

• Including parameter adjust in node_color_per_de function. Set TRUE as default, previously considered as FALSE

• Allowing node_colors_per_de to accept any experimental design accepted by limma::makeContrasts.

• Removing non-visible function compute_difexp

• Adding GO IDs to GO annotations and making them the rownames of the go_vals matrix

• Adding get_go_names function, to translate GO Ids to GO function names

• Adapting to new RData names in AnnotationHub, which include the version of the data in hpAnnot files.

• Restricting GO names to 50 characters.

• Adding group.by slot to metaginfo objects.

HIREewas

             Changes in version 1.0.1 (2018-11-18)                  

• Corrected the title of vignettes

HPAanalyze

                     Changes in version 1.1                         

• Changes in version 1.1.5 + Reformatted NEWS file.

• Changes in version 1.1.4 + Added the query vignette.

• Changes in version 1.1.3 + Fixed issues where hpaVis and hpaXml give faulty output. + All hpaVis functions as well as hpaListParam and hpaSubset now use the bundled dataset by defauft if no data argument is specifed. + All hpaVis functions now have default for all of their arguments and will create a warning message when the defaults are used. + The in-depth vignette was rewritten, and new vignettes added for ease of use. + Updated the themes of hpaVis functions for better clarity. + Updated documentations. + Hex sticker is now available.

• Changes in version 1.1.1 + HPAanalyze now uses openxlsx for hpaExport() instead of XLConnect.

• Changes in version 1.1.0 + Starting devel for Bioconductor 3.9

hpar

                    Changes in version 1.25                         

Changes in version 1.25.1

• Update to HPA release 18.1 <2019-01-21 Mon>

Changes in version 1.25.0

• New release for Bioconductor devel 3.9

HTSFilter

                   Changes in version 1.23.1                        

• – Add ImmunoOncology to biocViews in DESCRIPTION

ideal

                    Changes in version 1.8.0                        

New features

• plot_ma gains an additional parameter, labels_repel, for better placing the labels on the features to mark - The pairwise correlation plots can now use logarithmic scale in the axes, use smaller subsets of the data for quicker inspection, and resizes the correlation info proportionally to its intensity - The id types can now be chosen among the keytypes of the corresponding annotation packages (which still need to be installed when ideal is launched). Other input fields that specify id types also behave in a similar manner (e.g. in the Signature Explorer tab). This caused a problem for scenarios where common id types such as ENSEMBL are not available, like in Arabidopsis (where ids are provided often as TAIR) - thanks to Marc Galland for picking this up in https://github.com/federicomarini/ideal/issues/1 - The Signatures Explorer tab also has a fully fledged tour for first-time users, together with a collapsible help panel to describe its functionality in brief - The zoomed MA-plot gains a new widget to control the labels size for the names of the genes - It is possible to export the input data together with the results in a combined SummarizedExperiment object, which can be seamlessly fed into iSEE (http://bioconductor.org/packages/release/bioc/html/iSEE.html). This leverages a new function, wrapup_for_iSEE, which is available and exported from ideal.

Other notes

• An information box has been added to provide detailed information on the required input formats - Added notification to specify how to install the airway package for demonstration purposes if not already available - The Signatures Explorer tab is now displayed in a conditional panel, i.e. only when the required inputs are provided

infercnv

             Changes in version 0.99.8 (2019-04-20)                 

• Fix missing labels on heatmap due to change in how axis() handles overlaps.

• Improve auto thresholding of heatmap colors to still work when using stronger denoise settings.

• Updated some examples to use tempfile() for output.

• Fix duplicate piece of code that produced an error when using plot_steps.

             Changes in version 0.99.0 (2019-03-15)                 
  

• Submitted to Bioconductor

InPAS

                   Changes in version 1.15.2                        

• update author’s email.

                   Changes in version 1.15.1                        
  

• add the new biocViews tag “ImmunoOncology”

INSPEcT

                   Changes in version 1.12.1                        

• major update of INSPEcT, which now handles additional functions and analysis, such as: (i) extracting RNA dynamics from only total RNA-seq data, (ii) assessing differential regulation between steady states with an improved statistics, (iii) assessing the burden of the processing rate step in the responsiveness of mature RNA.

• minor updates regard the estimation of the variance from replicates, that now uses the package “DESeq2” (when read counts are available) or “plgem” (when only expression data is available) ######## the INSPEcT datasets older than this version are NOT COMPATIBLE anymore ############## ######## and must be updated using the function “convert_ids”, available in the ############## ######## “inst” folder of the package. Usage: ############## > source(file.path(system.file(package=’INSPEcT’), ‘convert_ids.R’)) > new_ids <- convert_ids(old_ids, degDuringPulse=c(FALSE,TRUE))

IntEREst

                    Changes in version 1.8.0                        

NEW FEATURES

• interest() and interest.sequential() functions support the possibility to define other parameter settings of BamFile() function of Rsamtools package e.g. “qnamePrefixEnd” and “qnameSuffixStart”.

• annotateU12() can return the PWM match scores (if requested). The hybrid AT-AG and GT-AC U12 types can be set to be ignored. The introns/exons coordinates can be filtered according to their map to another set of coordinates.

BUG FIXES

• referencePrepare() just gives warning and continue without annotating gene names (when annotateGeneIds=TRUE parameter is set) if annotating with gene names is not possible.

• interest() used to return Error if single end mapped reads did not existed at all (despite being requetsed). This has been corrected.

IRanges

                   Changes in version 2.18.0                        

NEW FEATURES

• Add some methods for CharacterList derivatives (nchar, substring, substr, chartr, toupper, tolower, sub, gsub, grepl).

BUG FIXES

• Fix unlist() on a SimpleRleList object of length 0

• Fix drop() for FactorList derivatives

• Fix removed rownames upon replacing in a SplitDataFrameList

DEPRECATED AND DEFUNCT

• Deprecate RangedData objects. The use of RangedData objects has been discouraged in favor of GRanges or GRangesList objects since BioC 2.12, that is, since 2014. Developers are required to migrate their code to use GRanges or GRangesList instead of RangedData objects (the GRanges and GRangesList classes are defined in the GenomicRanges package).

• Several RangedData methods are now defunct (after being deprecated in BioC 3.8): - score, score<-, lapply, within, countOverlaps; - coercions from list, data.frame, DataTable, Rle, RleList, RleViewsList, IntegerRanges, or IntegerRangesList to RangedData.

iSEE

                    Changes in version 1.3.9                        

• Add ORCID identifiers.

• Fix subscript error when tables receive a selection.

• Fix panel names in panel organization selectize input.

• Control the application of panel organization updates using an action button.

• Fix child replotting upon lasso close.

• Fix code reporting for zero-length DataFrame

                    Changes in version 1.3.8                        
  

• Support multiple selections.

• Avoid Javascript error with check group conditional.

                    Changes in version 1.3.7                        
  

• Add ImmunoOncology in biocViews.

                    Changes in version 1.3.6                        
  

• Control point size.

                    Changes in version 1.3.5                        
  

• Additional information during the default tour.

                    Changes in version 1.3.4                        
  

• Fix panel organization selectize.

                    Changes in version 1.3.3                        
  

• Update default tour steps to match updated user interface.

• Parse quote symbols literally in default tour steps.

• Fix name-to-index conversion of feature names for heat map panel.

                    Changes in version 1.3.2                        
  

• Move panel organization to modal with selectize to control panel display and ordering, remove sidebar.

• Add control of width and height of new panels.

• Enable voice control.

• Refactor internal functions.

                    Changes in version 1.3.1                        
  

• Fix invalid row index sent from tables in RStudio browser.

• Fix initialization of search fields for tables that are initialized with an incoming selection.

• Fix constant field name.

IsoCorrectoR

                    Changes in version 1.0.3                        

• added automated code testing with testthat

• fixed typo in ‘biocViews’ field of DESCRIPTION

                    Changes in version 1.0.1                        
  

• Fixed an issue where correction would abort with an error message if chemical formulas in the molecule file contain Phosphorus (thanks to Mathieu Bousquet for reporting this)

• Fixed an issue that could lead to an error if measurement IDs in the measurement file are a suffix of other measurement IDs (e.g., cysteine_1 and homocysteine_1)

• The display of error messages in the R console (they always appear in the log file) is now no longer suppressed if verbose is set to FALSE in the IsoCorrection() function call

IsoCorrectoRGUI

                    Changes in version 0.0.1                        

• prepare for Biocoductor submission

IsoformSwitchAnalyzeR

• NEWS file couldn’t be formatted. Please see the link to the NEWS file on the package landing page for complete details

isomiRs

                   Changes in version 1.11.3                        

FEATURES

• Combined samples and create new object. Useful for technical replicates.

• Add isoAnnotate function to get more information for each isomiR.

• Add isomiR naming and sequences table in metadata of object.

• Remove reference sequences from isoPlot figures.

• Support filtering isomiRs with low % of importance (statistically supported).

• Support isoPLot to use only certain isomiRs.

                   Changes in version 1.11.2                        
  

FIX

• Fix NEWS format.

• Fix documentation typos.

FEATURES

• Filter isomiRs by importance ratio.

• Allow to plot selected isomiRs with isoPlot function.

karyoploteR

                   Changes in version 1.10.0                        

NEW FEATURES

• Added new color managements functions including is.color and transparent and improved the existing ones.

• Added new functions to color data elements based on different features: chromosome, position, overlapping of regions…

• Improved gene and transcript plotting functions. Added functions to automatically get gene symbols from OrgDb objects. Improved transcript and gene positioning. Added a function to merge all transcripts of a gene into one.

• kpPlotBigWig can now adjust the ymax value based on the global maximum, per chromosome or taking into account only the visible region.

SIGNIFICANT USER-VISIBLE CHANGES

• It is now posible to add labels to the right-hand side of chromosomes with kpAddLabels

• Improved documentation and vignette

• makeGenesDataFromTxDb does not need a karyoplot anymore. Changed parameter order.

BUG-FIXES

• It is now possible to use cex in plotKaryotype to specify chromosome name sizes

• Multiple small bug fixes

KEGGprofile

                   Changes in version 1.25.1                        

• Fix bugs in download_KEGGfile function.

KinSwingR

             Changes in version 1.0.4 (2019-04-24)                  

• correction to pseudo count in scorePWM and viewPWM

• added option of motif coloring by AA properties to viewPWM

• update vignette

             Changes in version 1.0.3 (2018-11-12)                  
  

• Bug in network output from swing fix

             Changes in version 1.0.2 (2018-11-09)                  
  

• Making viewPWM visible

             Changes in version 1.0.1 (2018-11-05)                  
  

• Fixed bugs - matrix division in swing() and labels in buildPWM

• input_data in outputs of ScoreSequences - to trace trimmed sequences

limma

                   Changes in version 3.40.0                        

• Major rewrite of arrayWeights() to improve speed and stability. The arrayWeightsSimple() function has been removed and its functionality incorporated into arrayWeights(). A new ‘var.group’ argument has been added to simplify specification of the variance design matrix. The weights are now squeezed slightly towards unit and a new argument ‘prior.n’ has been added to control the prior weight with which the array weights are squeezed. arrayWeights() now chooses between the REML and gene-by-gene algorithms automatically by default. REML is chosen when there are no prior weights or missing values and gene-by-gene is used otherwise. arrayWeights() now checks for and skips over any genes with zero residual variances.

• voom() now checks for experiments that have no replication. In this case it now returns weights that are all 1, with an informative warning but no error. Two references have been added to the voom help page.

• classifyTests.Rd now focuses on nested F-tests. The function FStat() is now removed. It was a convenience wrapper for classifyTestsF() with fstat.only=TRUE but is not used often enough to justify itself. classifyTestsP() is no longer exported as it is not intended to be called by users. The function classifyTestsT() is now removed, having been superceded by more sophisticated multiple testing methods.

• contrasts.fit() now removes any test statistics or p-values found in the fit object. This avoids any potential mis-match between coefficients and test statistics if eBayes() has been run on the object previously.

  More details have been added to the warning about approximations in the contrasts.fit() help page.

• The old function ebayes(), which was deprecated a year ago in favor of eBayes(), is now removed.

• The fitted() and residuals() methods for MArrayLM objects now give an informative error message if the object contains contrasts instead of the original coefficients.

• Rewrite Filtering chapter of User’s Guide.

• Add Research Fields to the biocViews entry in the package DESCRIPTION file.

maftools

                    Changes in version 2.0.0                        

SIGNIFICANT USER-LEVEL IMPROVEMENT

• Oncoplot, oncostrip and coOncoplot code has been migrated from ComplexHeatmap to base graphics. Default values for some arguments have been changed.

• Changed default value for mafObj argument in subsetMaf to TRUE. Issue: #235

• All ggplots are migrated to base graphics for consistancy

• TCGA mutations per sample used for tcgaCompare are updated to more stable MC3 cohort from deprecated broad firehose.

IMPROVEMENTS

• tcgaCompare now accpets comparing against user specifc cohorts. Issue: #229

• Add missing genes and samples to oncoplot even when they are not altered. Issue: #254

• Added MTRNR2L8 protein structure to pfam database. Issue: #255

• Added addtionalFeature argument to oncoplots. Issue: #270

• Added log scale option for summary and oncoplots. Issue: #273

• Made protein domain db compatible with R version < 3.5 Issue: #276

• Added draw draw_titv, and exprsTbl argument to oncoplot

• Additional edits with TMB visualization and additionalFeatures Issue: #289

• Cooncoplot improvements Issue: #296

BUG FIX

• Oncoplot annotationOrder bug fix. Issue: #293

• Update code for AnnovarToMaf. PR #288, #234

• fixed handling of Status in survival. PR #274

• Fix swapped confidance intervals in mafCompare function Issue: #269

• update docs, and vectorized code Issue: #266 #267

• Improve oncoplot annotations for numeric class Issue: #263 and #203

• In annovarToMaf read the .tsv file considering the header. PR #259

• Fix legend title order. Issue: #253

• GISTIC sample size issue fix. Issue: #249

• Bug fix for oncoplots with CNV data. Issue: #240

• Better error handling in plotApobecDiff with no SMGs. Issue: #232

• Bug fix that caused signature extraction to terminate in case of zero mutations. Issue: #228

• Bug fix due to missing levels contingency tables in clinical enrichment. Issue: #225

• Add showTumorSampleBarcodes to PlotOncogenicPathways. Issue: #214

• Cleanup docs for Oncoplot. Issue: #207

• Implemented isNumeric and groupAnnotationBySize to improve sorting. Issue: #207

• Fix ComplexHeatmap update. Issue: #205 #210

• plotmafSummary addStats bug fix Issue: #204

• Rainfall plot data.table null fix. Issue: #201

• Support non human BSgenome. Issue: #197

• SampleID bug fix. Issue: #153

MAGeCKFlute

                    Changes in version 1.2.2                        

• Revise ReadRRA function.

• Add ReadsgRRA function to read sgrna_summary in MAGeCK RRA results.

• Add sgRankView function to visualize the rank of sgRNA targeting top selected genes.

• Remove bugs in FluteMLE and FluteRRA.

• Add additional visualization functions in FluteRRA.

• Add EnrichedGeneView to visualize the core enriched genes in enriched pathways.

• Integrate WikiPathways, PID terms and EHMN pathways into enrichment functions.

• Export all the hidden functions.

                    Changes in version 1.2.1                        
  

• Add VolcanoView to show positive and negative selected genes.

• Improve EnrichedView and EnrichedGSEView function.

• Add QC figures in vignettes.

• Merge MsigDB, KEGG, and GO genesets together and integrate them into package.

matter

                   Changes in version 1.9.11                        

BUG FIXES

• Fixed documentation link to ‘base::lapply’

             Changes in version 1.9.10 (2018-12-22)                 
  

SIGNIFICANT USER-VISIBLE CHANGES

• Vectors can be used as ‘virtual_mat’ rows/columns now

             Changes in version 1.9.9 (2018-12-22)                  
  

SIGNIFICANT USER-VISIBLE CHANGES

• Constructor for ‘drle’ now allows forcing delta = 0

• Updated display descriptions in ‘show’ methods

• Check for NULL dimensions when subsetting ‘virtual_mat’ and ‘sparse_mat’ classes

             Changes in version 1.9.8 (2018-12-18)                  
  

BUG FIXES

• Check for NULL dimensions in ‘matter_arr’ subsetting

             Changes in version 1.9.7 (2018-12-18)                  
  

BUG FIXES

• Fixed bug in atoms() where ‘index_offset’ and ‘index_extent’ would overflow when creating long ‘matter_vec’ objects

             Changes in version 1.9.6 (2018-12-14)                  
  

SIGNIFICANT USER-VISIBLE CHANGES

• Subsetting matter matrices, arrays, and data frames now checks for the correct number of dimensions

• Linear indexing support for ‘matter_mat’ and ‘matter_arr’

BUG FIXES

• Class checks now use R_check_slot_etc() in C so subclasses of ‘matter’ objects should inherit correct behavior

• Fixed other indexing issues in subsetting + assignment

             Changes in version 1.9.5 (2018-12-14)                  
  

SIGNIFICANT USER-VISIBLE CHANGES

• Updated documentation with matter-datatypes, size of data types are now explicitly defined

• Changed ‘filemode’ slot to be a factor with levels c(‘r’, ‘w’, ‘rw’) instead of a string

• Data access now uses C++ fstream instead of C

BUG FIXES

• On Windows, accessing data elements in large files with byte offets larger than MAX_INT now works

• On Windows, data modes of ‘long’ and ‘ulong’ are now correctly 64-bit integer types

• Assignment of negative values now checked for ‘ulong’

                    Changes in version 1.9.4                        
  

NEW FEATURES

• Added %% and %/% delayed operations from Arith group

• Added & and

  delayed operations from Logic group

• All Ops group generics now supported as delayed operations

• Added ‘lapply’ and ‘sapply’ functions for ‘matter_list’

• Support for BiocParallel in ‘apply’, ‘lapply’, and ‘sapply’

BUG FIXES

• Fix floating point exception error when dividing by integer 0L in delayed division operations

                    Changes in version 1.9.3                        
  

NEW FEATURES

• Added matrix multiplication for ‘sparse_mat’ matrices

• Added matrix multiplication for ‘virtual_mat’ matrices

             Changes in version 1.9.2 (2018-11-12)                  
  

BUG FIXES

• Renamed internal class ‘bytes’ to ‘num_bytes’ due to Rcpp

             Changes in version 1.9.1 (2018-11-12)                  
  

BUG FIXES

• Removed BiocGenerics ‘lengths’ from NAMESPACE

             Changes in version 1.8.2 (2018-12-13)                  
  

BUG FIXES

• Fixed large file offset bug on Windows (again)

             Changes in version 1.8.1 (2018-12-11)                  
  

BUG FIXES

• Fixed bug causing large files to read incorrectly on Windows

mbkmeans

             Changes in version 0.99.0 (2019-03-08)                 

• This is the pre-submission version.

• Change default in mbkmeans to use a batch size equal to 5% of the data.

• Change default in mbkmeans to max 100 iterations.

• Fix blocksize() to work if impossible to calculate available ram.

Melissa

                   Changes in version 0.99.0                        

• First package release. News and details of updates will be added in future releases.

metagene2

             Changes in version 1.1.0 (2019-04-05)                  

• Submitted package to Bioconductor.

metagenomeSeq

                    Changes in version 1.25                         

• Added ‘wrenchNorm’ function

• Added option to use IHW as p-value adustment method in ‘MRcoefs’

• Modified ‘expSummary’ slot in ‘MRexperiment’ object to be of class ‘list’ instead of ‘environment’

MetaNeighbor

                    Changes in version 1.3.0                        

• Added memory efficient version of MetaNeighbor and MetaNeighborUS

• Added supporting functions for memory efficient versions

MetCirc

             Changes in version 1.13.1 (2019-04-04)                 

• check if package passes R CMD build and R CMD check without any error messages and vignette can be run without any errors

methimpute

                    Changes in version 1.5.2                        

BUGFIXES

• Removed runnable example from exportMethylome() because of memory issues with data.table::fwrite() since Bioconductor 3.9.

methylGSA

                    Changes in version 1.1.5                        

• Parallel option is supported

                    Changes in version 1.1.1                        
  

• Fixed typos in vignettes - Included citation

methylKit

                    Changes in version 1.9.4                        

NEW FUNCTIONS AND FEATURES

• calculateDiffMeth: introduce method “midPval” for fast testing of different methylation if there is one sample per group, contributed by @zellerivo

IMPROVEMENTS AND BUG FIXES

• calculateDiffMeth: - fix rare case issue with invalid p-values on calculateDiffMeth call, that caused “qvalue” p-value adjustment to fail https://github.com/al2na/methylKit/issues/90 - let user choose between new “midPval” or older “fast.fisher” implemtation for statistical test used to determine the methylation differences https://github.com/al2na/methylKit/issues/96 - introduce p-value lookup table to reduce multiple testing of identical configurations https://github.com/al2na/methylKit/issues/96 - reduce code duplication and overhead by introducing S3 functions to be called by S4 methods

• update vignette with section about usage of methylKit for analysis of affinity- and array-based methylation assays

• methSeg: if object with multiple chromosomes is used, remove chroms with less than two ranges

• unite: fix issue where digits were written in scientific notation https://github.com/al2na/methylKit/issues/130

• getCorrelation: fix issue where getCorrelation produces matrix with NA when using “min.per.group” https://github.com/al2na/methylKit/issues/137

                    Changes in version 1.9.3                        
  

IMPROVEMENTS AND BUG FIXES

• getCorrelation: reduce code duplication and overhead by introducing S3 functions to be called by S4 methods

• fread.gzipped: rewrite building of shell command with system2 to mimic R.Utils::gunzip

• improve validity checks for methylDB objects

• pool: check length of treatment and number of sample is same

• headTabix: use fread.gzipped only when user wants to get more than 1e6 rows

• test-1-read: check if methylRawDB is same when directory is given or not, i.e. test wether directory affects object

• methylRaw: check for content in tabix file, break if not

• calculateDiffMeth: dealing with case of full model not being different from reduced model; print warning and set NaN to 1

• pool: check length of treatment and number of sample is same

• improve validity checks for methylDB objects

                    Changes in version 1.9.2                        
  

IMPROVEMENTS AND BUG FIXES

• fread.gzipped: update function to check compression based on file content and allow to decompress .bgz files

• headTabix: use fread.gzipped directly on the tabix file fixes issue https://github.com/al2na/methylKit/issues/141

                    Changes in version 1.9.1                        
  

IMPROVEMENTS AND BUG FIXES

• add methylRawListDB constructor fixes https://github.com/al2na/methylKit/issues/134

• update validation functions for methylRaw/methylRawDB: check for single sample id

• unite: write S3 functions for class methylRawList and methylRawListDB Fixes https://github.com/al2na/methylKit/issues/132

methylPipe

                   Changes in version 1.17.1                        

• updated or fixed the following functions: + getCposDensity : fixed the warning message in checking for NA in a list

MetNet

             Changes in version 1.1.2 (2019-04-16)                  

• check that MetNet passes all builds without any errors or warnings

             Changes in version 1.1.1 (2019-04-03)                  
  

• correct typo in vignette

MGFR

                    Changes in version 1.9.2                        

• Added an argument class.vec to the function getMarkerGenes.rnaseq() to provide the classes of samples in the data matrix

• Changed default of the argument annotate to FALSE

• Fixed an error caused when no markers are found

microbiome

             Changes in version 1.5.4 (2018-11-20)                  

• Fixed bug in merge_taxa2

• Fixed bug in Pielou’s evenness

• New functions: readcount, bfratio, aggregate_top_taxa

• rewritten aggregate_taxa and moved the top argument in the new function aggregate_top_taxa

• plot_composition function: new options for sample.sort and otu.sort

• Added Phylum level to taxonomy tables in example data sets * New function: dominant

• The diversities function is now replaces by alpha function. The alpha is more generic and can return also other alpha diversity indices.

• plot_frequencies function now only returns the ggplot object

• Renamed the global function into alpha

• Renamed arguments rarity.detection and rarity.prevalence into detection and prevalence in the rarity function

• Added Chao1 index in richness function

• In atlas1006 data set, pseudocount of +1 in otu table has been removed to facilitate comparison with sequencing data sets and to avoid confusion

• In atlas1006 data set, only a single replicate per subject-time combination is chosen (at random)

• New function collapse_replicates has been added

• Abundance matrices (otu tables) for all example data sets now starting from 0 without pseudocount

• Changed the default for the detection argument in the richness function to detection=0

• removed rarity.threshold and rarity.prevalence options from the alpha function

• Various minor fixes; see github commits for many more details o Color order in plot_landscape legend now follows the factor levels of the col argument o Fixed example in remove_samples

minfi

                    Changes in version 1.29                         

• v1.29.4 Fixed a bug in detectionP where the function always returned NA for a 27k array. Reported by Laurenz Holcik.

• v1.29.4 Fixed a bug in preprocessNoob where the function would error when supplied an input data set with only 1 sample (when using default arguments). Reported by Matt Oldach.

miRSM

                    Changes in version 1.1.4                        

• Update imports <2019-04-19, Fri>

                 Changes in version 1.1.1-1.1.3                     
  

• Update miRSM.R <2019-03-08, Fri>

miRsponge

                    Changes in version 1.9.3                        

• Update the Groundtruth <2019-03-13, Wed>.

                    Changes in version 1.9.2                        
  

• Rename the miRsponge package called miRspongeR, and add zzz.R file to points users to the new package ‘miRspongeR’ <2019-03-07, Thur>.

Modstrings

             Changes in version 0.99.0 (2019-01-15)                 

• Submitted to Bioconductor

MOFA

             Changes in version 0.99.0 (2019-01-25)                 

• Submitted to Bioconductor

motifStack

                   Changes in version 1.27.5                        

• change plotMotifLogo to grob.

                   Changes in version 1.27.4                        
  

• Update authors information.

• change the d3-tip background color.

• adjust the fontsize to remove the gaps.

• change the title position.

                   Changes in version 1.27.3                        
  

• use grImport2 instead grImport to avoid the installation of ghostscript.

                   Changes in version 1.27.2                        
  

• add knitr in vignettes to pass window’s builder

                   Changes in version 1.27.1                        
  

• try to pass window’s builder

mpra

                    Changes in version 1.5.3                        

• Update main paper citation.

• Update vignette with better examples for allelic studies.

• Add mpraSetAllelicExample to available data.

MSnbase

                     Changes in version 2.9                         

Changes in version 2.9.6

• remove plain NEWS file now that R supports NEWS.md

Changes in version 2.9.5

• Add isolationWindowLowerMz and isolationWindowUpperMz methods <2019-04-15 Mon> - Add filterPrecursorMz method <2019-04-15 Mon> - Add filterIsolationWindow method <2019-05-16 Tue>

Changes in version 2.9.4

• Remove NAnnotatedDataframe <2019-04-10 Wed>

Changes in version 2.9.3

• Fix bug in ms2df (order of fcols could be scambled) <2018-12-04 Tue> - Fix bug in MSnSet constructor (see issue #386) <2018-12-07 Fri> - Add filterPolarity method (see issue #388, feature requeste by @zeehio) <2018-12-10 Mon>

Changes in version 2.9.2

• Fix problem that impute(x, method=”knn”) sets the seed (issue #380). Contributed by Constantin Ahlmann-Eltze <2018-11-16 Fri> - Conserve spectra names in combineSpectra (see #379) <2018-11-15 Thu>
• Fix bug in writeMSData - see #383 <2018-11-22 Thu>

Changes in version 2.9.1

• Add clean,Chromatograms (issue #354) <2018-11-07 Wed> - Add as,Spectra,list as,Spectra,MSnExp and as,MSnExp,Spectra (issue #370) <2018-11-07 Wed> - Add filterMsLevel,Spectra <2018-11-07 Wed> - Fix regression bug in plot,Spectrum1 <2018-11-14 Wed>

Changes in version 2.9.0

• New version for Bioc 3.9 devel

MSnID

                   Changes in version 1.17.1                        

• Broadened the scope of the tool to ImmunoOncology - that is finding rare events that reflected in protein sequence.

msPurity

                   Changes in version 1.9.12                        

• Troublshoot mac “[MSData::Spectrum::getMZIntensityPairs()] Sizes do not match” error

                   Changes in version 1.9.11                        
  

• Bug fix for createMSP - now handles metada with duplicate grpids

                   Changes in version 1.9.10                        
  

• Documentation updates

                    Changes in version 1.9.9                        
  

• NEW FUNCTION: createDatabase + Updated version of create_database that uses an updated schema

• NEW FUNCTION: spectralMatching + Updated version spectral_matching that allows for more flexibility

• Vigenettes and documentation update

                    Changes in version 1.9.8                        
  

• NEW FUNCTION: filterFragSpectra (for purityA objects) + LC-MS/MS filtering of spectra (prior to averaging)

• NEW FUNCTIONS: averageIntraFragSpectra, averageInterFragSpectra, averageAllFragSpectra (for purityA objects) + LC-MS/MS averaging and filtering functionality

• NEW FUNCTION: createMSP + Create msp files from purityA objects where XCMS features have been linked to fragmentation spectra

• Updated create_database and spectral matching to have the option to use averaged fragmentation spectra

                    Changes in version 1.9.2                        
  

• Bug fix for groupPeaks and groupPeaksEx (the ppm argument was not working and there was inconsistent behaviour with larger datasets). Thanks to Elliot for spotting (https://github.com/litepalmer)

• Updated documentation for spectral matching

mzR

                   Changes in version 2.17.4                        

• Update documentation, pointing to MSnbase rather than directly use low-level classes. <2019-04-17 Wed>

                   Changes in version 2.17.3                        
  

• Extract isolation window from mzML files (issue #193): data.frame returned by header gains columns “isolationWindowTargetMZ”, “isolationWindowLowerOffset”, “isolationWindowUpperOffset”.

                   Changes in version 2.17.2                        
  

• Fix bug #185: Error in R_nc4_open: Too many open files

NADfinder

                    Changes in version 1.7.4                        

• Fix the warning of documentation of computeLibSizeChrom.

                    Changes in version 1.7.1                        
  

• Update author email.

NBAMSeq

             Changes in version 0.99.1 (2019-02-13)                 

• Package created

NBSplice

                    Changes in version 1.1.1                        

• DESCRIPTION: Adding ImmunoOncology as a BiocView tag

netboost

              Changes in version 0.99 (2019-04-02)                  

• Final submission changes for Bioconductor.

NetPathMiner

                   Changes in version 1.19.1                        

• Added a new function to create a metabolite network.

• Added a new function to reindex networks using vertex attributes.

• Removed compiler warnings.

• Fixed various bugs in network manipulation.

ngsReports

             Changes in version 0.99.8 (2019-04-03)                 

• This is a breaking change! Significant changes to most functions have been implemented

• Extracting modules is no longer performed by individual functions, but is now performed using the function getModule

• FastqcFileLists objects are no longer defined and the class FastqcFile has been made into the private class .FastqcFile

• FastqcDataList objects have names attributes and can now be subset using names

• The function fileName has been renamed as fqName to clarify that it refers to the underlying Fastq file for a Fastqc report

• All log file imports are now handled by the single function importNgsLogs

• Most plot functions have been renamed with shorter names, e.g. plotOverrepresentedSequences is now plotOverrep

• The FastQC version is now obtained using fqcVersion not Version

• The functions genomes() and transcriptomes() have been removed and this information is now obtained using gcAvail(object, type)

• The function getGcDistn() has been renamed as estGcDistn() to avoid any confusion with getGC() which works on TheoreticalGC objects.

             Changes in version 0.99.1 (2019-02-03)                 
  

• Removed Remotes from DESCRIPTION

• Added getGcDistribution to enable calculation of GC Content Distributions from FastaFiles

             Changes in version 0.99.0 (2019-02-01)                 
  

• Submitted to Bioconductor

• Shiny App has been moved to a separate package, located at https://github.com/UofABioinformaticsHub/shinyNgsReports

OmaDB

             Changes in version 1.99.3 (2019-04-15)                 

• update format of NEWS file

             Changes in version 1.99.2 (2019-03-13)                 
  

• re-license under GPLv3

• updated ipython notebook with examples from manuscript to new release of OMA browser

• improve package according to bioconductor guidelines: o improve README and DESCRIPTION o various cleanups of code and data

             Changes in version 1.99.1 (2018-12-28)                 
  

• fixes bioconductor CI warnings on missing links in deprecated functions

             Changes in version 1.99.0 (2018-12-21)                 
  

• major refactoring of codebase: o getData split into getProtein, getGenome, getOMAGroup o renamed getAnnotation -> annotateSequence o renamed getXref -> searchSequence

• getProtein allows to retrieve many protein ids at once

• improved documenation by a lot.

OmicsLonDA

                   Changes in version 0.99.10                       

• Fix FeatureSpline plots in README and vignette

                   Changes in version 0.99.9                        
  

• Fix all CRAN and Bioconductor checks

                   Changes in version 0.99.1                        
  

• Submitted to Bioconductor

OncoSimulR

             Changes in version 2.13.2 (2019-03-18)                 

• changes in behavior of sample (see NEWS and https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17494) were leading to failures of some tests. Using RNGversion in some tests.

             Changes in version 2.13.1 (2019-02-07)                 
  

• bumped to one over the BioC-3.9 version

onlineFDR

                    Changes in version 1.1.3                        

MODIFICATIONS

• updated unit tests for LOND, bonfInfinite and LORDdep

                    Changes in version 1.1.2                        
  

MODIFICATIONS

• updated unit test for LORD

                    Changes in version 1.1.1                        
  

MODIFICATIONS

• added the LORD++ procedure for online FDR control

• updated references

• updated vignette

oposSOM

                    Changes in version 2.0.3                        

• Check for detected singleton spot modules implemented

                    Changes in version 2.0.2                        
  

• csv output for international spreadsheet format.

                    Changes in version 2.0.1                        
  

• Colored edges in sample correlation networks & minor fixes.

ORFik

                    Changes in version 1.3.7                        

SIGNIFICANT USER-VISIBLE CHANGES

• mapToGRanges is now much faster and uses much less memory. A c++ reimplementation of pmapFromTranscripts from GenomicFeatures.

OVESEG

             Changes in version 0.99.2 (2019-01-14)                 

• trigger version bump

             Changes in version 0.99.1 (2019-01-14)                 
  

• modifiy vignette to fix TIMEOUT build in MAC

             Changes in version 0.99.0 (2019-01-10)                 
  

• Submitted to Bioconductor

PAST

            Changes in version 0.99.19 (2019-04-22)                 

• bug fixes

• improvements to speed

            Changes in version 0.99.18 (2019-04-22)                 
  

• documentation updates and minor code clean-up

            Changes in version 0.99.17 (2019-04-18)                 
  

• updated pathways functions to reflect changes across other methods

            Changes in version 0.99.16 (2019-04-18)                 
  

• updated SNP function and added rtracklayer dependency

            Changes in version 0.99.15 (2019-04-17)                 
  

• renamed LD function and changed added column name specification

            Changes in version 0.99.14 (2019-04-16)                 
  

• renamed merge function and changed method of describing input type

            Changes in version 0.99.13 (2019-04-16)                 
  

• addressed description issues

            Changes in version 0.99.12 (2019-04-15)                 
  

• updated manual

            Changes in version 0.99.11 (2019-04-15)                 
  

• updated manual

            Changes in version 0.99.10 (2019-04-15)                 
  

• added types of data

             Changes in version 0.99.9 (2019-04-15)                 
  

• separated Shiny app

             Changes in version 0.99.8 (2019-04-15)                 
  

• corrected author list format

             Changes in version 0.99.7 (2019-04-15)                 
  

• corrected author list format

             Changes in version 0.99.6 (2019-04-11)                 
  

• corrected documentation

             Changes in version 0.99.4 (2019-04-08)                 
  

• updated vignette

• added filtering options to R Shiny app

             Changes in version 0.99.3 (2019-04-03)                 
  

• Corrected NEWS

• added vignette description

             Changes in version 0.99.2 (2019-02-28)                 
  

• Removed extra code

             Changes in version 0.99.1 (2019-02-28)                 
  

• Closed connections after finishing with them

             Changes in version 0.99.0 (2019-02-28)                 
  

• Submitted to Bioconductor

PathoStat

                    Changes in version 1.8.1                        

• Update data uploading

• Modify visualization

• Add biomarker tab

pathview

                   Changes in version 1.23.3                        

• fix error and warning cause by geneannot.map() function. change if(in.type == out.type) to if(all(in.type == out.type)). change biocLite installation to BiocManager::install. make similar changes in sim.mol.data() function.

• update NAMESPACE file on importFrom lines on AnnotationDbi and BiocManager.

pathwayPCA

                   Changes in version 0.99.1                        

2019-02-01

We are submitting to Bioconductor soon, so we are resolving as many of the BiocCheck() ERRORs, WARNINGs, and NOTEs. See https://github.com/gabrielodom/pathwayPCA/issues/64

                   Changes in version 0.98.0                        

2018-12-13

See the issues within the “Bioconductor Submission” and “Vignette Work” milestones for detailed descriptions of these changes, their discussion, and motivation: https://github.com/gabrielodom/pathwayPCA/issues

• Standardized naming conventions to UpperCamelCase for consistency - Changed class name pathwaySet -> pathwayCollection - Added functions SubsetPathwayData, getPathPCLs, LoadOntoPCs, write_gmt, getSampleIDs, CheckSampleIDs, getTrimPathwayCollection, getPathwayCollection, CheckPwyColl, CheckAssay, and print and subset methods for pathwayCollection objects - Added sample ID requirements for input assays and phenotype data. Changed the phenotype required class from anything to a data frame. - Made the lars implementation a touch more robust. If the algorithm fails to converge, then we default back to regular SVD - The AESPCA function can also return pathway-specific vanilla PCA. Also, we inspected the parametric p-values compared to the permutation-based p-values. They congruence is nearly perfect for all of the data sets we tested. Thus, we changed the default p-value estimation method for AESPCA to be parametric. - Method functions (*_pVals()) now return a list with the p-values data frame, list of PC vectors (in a data frame), and list of loading vectors (in a data frame). The getPathPCLs function will subset this list to return the PCs, loadings, and administrivia of the method PCA output for a single pathway - added the June homo sapiens pathway collection from WikiPathways: wikipwsHS_Entrez_pathwayCollection - Lily wrote a vignette geared to show off the diverse functionality of the package, so this is the new main vignette. I broke off the plots from chapter 4 into their own chapter. The five vignettes I wrote are now supplemental chapters - updated vignettes and website

                 Changes in version 0.0.0.9000                      
  

2018-03-20

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

pcaExplorer

                   Changes in version 2.10.0                        

New features

• Added extra parameters to topGOtable to offer more control on the method used, and the option to correct the p-values for multiple testing (via the Benjamini-Yekutieli procedure) - pca2go has now an option to return (early) a list with vectors of genes with high loadings - Better preview of the uploaded data with modal dialog windows triggered by buttons which appear once corresponding inputs are available - Improved notification system: in addition to the progress bar, info that all input is correctly specified, or suggest optional annotation loading - Added flexibility to select separator for each of the uploadable files - The pairwise correlation plots can now use logarithmic scale in the axes, use smaller subsets of the data for quicker inspection, and resizes the correlation info proportionally to its intensity - The sample to sample heatmap supports additionally manhattan and correlation-based distances - There is a new vignette with a detailed quick start, “Up and running with pcaExplorer”, specifying how the workflow with pcaExplorer can look like, demonstrated on the airway dataset - In the Instructions panel, we added buttons to access the fully rendered documentation, either local or online if e.g. deployed to a server. Related to this, pcaExplorer has a new parameter, runLocal, to control this behavior - An additional parameter, annopkg, has been added to pca2go() to override the behavior with the organism parameter (this is useful when the name of the annotation package is not conform to the classical org.Xx.eg.db, e.g. for Arabidopsis Thaliana); a detailed use case has been added in the main vignette

Other notes

• The computing of the required objects now requires the explicit action on the dedicated button, and the tooltip informs the user on what steps are taken (including normalization) - An information box has been added to provide detailed information on the required input formats - Added notification to specify how to install the airway package for demonstration purposes if not already available - Added startup message upon loading the package - The content in the Instructions tab is now contained in collapsible elements - The file formats accepted by pcaExplorer are now specified both in the vignette text, as well as in the app at runtime - The content of the Instructions tab is now more compact, containing the rendered “Up and running with pcaExplorer” vignette. The full vignettes can be accessed via buttons in the same panel - Added instructions to install phantomJS via the webshot package - would raise an error when previewing the report

PCAtools

                    Changes in version 1.0.0                        

• added new function getLoadings, which returns component loadings

PepsNMR

             Changes in version 1.1.3 (2019-03-11)                  

NEW FEATURES

• Added the ZeroFilling function

• Made the printed text for each pre-processing function optional

             Changes in version 1.1.2 (2019-03-08)                  
  

BUG CORRECTION

• Debugged Bucketing and InternalReferencing for n = 1

PGA

                   Changes in version 1.13.3                        

• Fix bug in function reportGear.R

                   Changes in version 1.13.2                        
  

• Fix bug in function reportGear.R

phantasus

                    Changes in version 1.3.5                        

• FGSEA tool

• Cache + static files optimizations

• Dataset permanent link feature

                    Changes in version 1.3.4                        
  

• Switch to fgseaMultilevel

                    Changes in version 1.3.3                        
  

• Custom order for annotation

• Revamped Charts tool

• AnnotationDB optimization

                    Changes in version 1.3.2                        
  

• PCA plot, GSEA plot and Chart tool can be exported to SVG

• Group by in column context menu

• Dataset open history

• Annotate dataset by AnnotateDB

• Switch column datatype in context menu

• GSEA plot uses general palette to color heatmap\annotation

• Minor bug fixes

piano

                    Changes in version 2.0.0                        

NEW FEATURES

• Added a function exploreGSAres() for interactively exploring the result object returned by runGSA(). This opens a Shiny app in a browser where users can view the different results tables and figures and get detailed information on specific gene-sets and genes.

• Added a function networkPlot2() that is an improvement to the old function networkPlot().

DOCUMENTATION

• Added a new vignette focused on gene-set analysis

Pigengene

             Changes in version 1.9.26 (2019-04-24)                 

Bug Fixes

• In the compute.pigengene function, if a module has only one gene, its name is now not omitted in the csv file.

             Changes in version 1.9.24 (2019-04-24)                 
  

Changes in existing functions

• An object of pigengene-class can now have a heavyToLow attribute.

             Changes in version 1.9.20 (2019-04-12)                 
  

Changes in existing functions

• In the compute.pigengene function, the columns of Data and names of modules can now differ.

             Changes in version 1.9.14 (2019-02-12)                 
  

Changes in existing functions

• The dOrderByW argument is now added for the compute.pigengene function.

             Changes in version 1.9.8 (2018-11-22)                  
  

Changes in existing functions

• All of the learn.bn function can now be set from one.step.pigengene through bnArgs.

             Changes in version 1.9.4 (2018-11-16)                  
  

Changes in existing functions

• gene.mapping can now output multiple conventions.

pipeFrame

             Changes in version 1.0.0 (2019-04-30)                  

• Bioinformatics R pipeline framework based on Bioconductor is released.

• Initial release version contains pipeline framework function elements including base class for each pipeline step, genome related data setting, global configuration, configuration initialization and pipeline flow chart management.

• Currently this framework is applied to package enrichTF.

             Changes in version 0.99.0 (2019-03-21)                 
  

• Submitted to Bioconductor

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)

PoTRA

            Changes in version 0.99.93 (2019-04-16)                 

• Updated the PoTRA algorithm

            Changes in version 0.99.92 (2019-04-16)                 
  

• Updated the PoTRA algorithm

            Changes in version 0.99.91 (2019-04-11)                 
  

• Removed examples section from the manual

            Changes in version 0.99.90 (2019-04-09)                 
  

• Added examples section to the manual

            Changes in version 0.99.89 (2019-04-09)                 
  

• Updated the usage section of the Rd document

            Changes in version 0.99.88 (2019-04-09)                 
  

• Updated the alias field in the Rd document

            Changes in version 0.99.87 (2019-04-09)                 
  

• Updated the lazy load field in the description file

            Changes in version 0.99.86 (2019-04-09)                 
  

• Edited the manual and updated the code in the .R files

            Changes in version 0.99.85 (2019-04-08)                 
  

• Edited the manual

            Changes in version 0.99.84 (2019-04-08)                 
  

• Edited documentation

            Changes in version 0.99.83 (2019-04-08)                 
  

• Edited script and exported function

            Changes in version 0.99.82 (2019-04-08)                 
  

• Removed R file

            Changes in version 0.99.81 (2019-04-08)                 
  

• Edited the manual

            Changes in version 0.99.80 (2019-04-07)                 
  

• Edited the manual

            Changes in version 0.99.79 (2019-04-07)                 
  

• Edited the manual

            Changes in version 0.99.78 (2019-04-07)                 
  

• Edited the manual

            Changes in version 0.99.77 (2019-04-06)                 
  

• Made minor edit to the PoTRA algorithm

            Changes in version 0.99.76 (2019-04-06)                 
  

• Made minor edits to the vignette

            Changes in version 0.99.75 (2019-04-06)                 
  

• Added a data object to the package

            Changes in version 0.99.74 (2019-04-03)                 
  

• Updated the package install instructions in the vignette

            Changes in version 0.99.73 (2019-04-03)                 
  

• Improved the code in the vignette and edited the manual

            Changes in version 0.99.72 (2019-04-02)                 
  

• Updated the landing page abstract

            Changes in version 0.99.71 (2019-04-02)                 
  

• Added devtools install script for repmis in vignette

            Changes in version 0.99.70 (2019-04-01)                 
  

• Accepted to Bioconductor

             Changes in version 0.99.0 (2019-02-21)                 
  

• Submitted to Bioconductor

pqsfinder

                     Changes in version 2.0                         

NEW FEATURES

• The qsfinder algorithm is ~100 times faster on real-world sequences than before. The main idea of the optimization is to stop the exhaustive search when we are sure there can’t be found better PQS. The optimization is applied only in non-overlapping mode.

• New boolean argument called “deep”. Once set to TRUE, pqsfinder will disable optimizations and run full exhaustive search.

SIGNIFICANT USER-VISIBLE CHANGES

• Default minimal PQS score was increased from 26 to 52. The score 52 shows the best balanced accuracy on G4 sequencing data provided by Chambers et al. 2015.

BUG FIXES

• Fixed resolution of overlapping sequences. When multiple same-scoring PQS overlap, the shortest one is chosen.

pram

                   Changes in version 0.99.17                       

• pram is in Bioconductor

                   Changes in version 0.99.13                       
  

• First release

profileplyr

             Changes in version 0.99.0 (2019-03-29)                 

• Submitted to Bioconductor

pRoloc

                    Changes in version 1.23                         

Changes in version 1.23.4

• Remove plain NEWS now that R supports NEWS.md

Changes in version 1.23.3

• Link to TAGM F1000 workflow <2019-04-11 Thu> - Add ref to TAGM F1000 in CITATION and README <2019-04-11 Thu> - Update biomart interface data and AnnotationParams-related code <2019-04-12 Fri>

Changes in version 1.23.2

• Add mcmc helper functions. - New logPosteriors accessor for MAPParams object. - New plotConsProfiles function, contributed by Tom Smith (see PR #131). - Update TAGM vignette, refering to workflow <2019-03-14 Thu>

Changes in version 1.23.1

• Add note about missing data in QSep man <2018-10-31 Wed> - Add mcmc-helper documentation <2018-11-04 Sun> - Fixing numerical instability in Cholesky decomposition (see #124) <2018-11-30 Fri> - Add option to display or not display grid in plot2D <2018-12-12 Wed>
• mrkHClust now uses mrkConsProfiles and returns the hclust object - see issue #130 for details and background <2018-12-19 Wed>

Changes in version 1.23.0

• New version for Bioc 3.9 devel

PureCN

                   Changes in version 1.14.0                        

NEW FEATURES

• support for copynumber package and its multisample segmentation

• beta support for PSCBS weighting

• support for gene symbol filtering in FilterCallableLoci.R (e.g. –exclude “^HLA”)

• added segmentationHclust function that clusters provided segmentation using log2-ratio and B-allele frequencies

• min.target.width and small.targets in preprocessIntervals to automatically deal with too small targets

• calculate confidence intervals for cellular fractions

• throw additional warning when sample is flagged as NON-ABERRANT and pick the diploid solution with lowest purity as best

SIGNIFICANT USER-VISIBLE CHANGES

• significant runtime improvements

• callLOH now reports all segments, even if there are no informative SNPs since some users were not aware that segments are missing from this output. Use keep.no.snp.segments = FALSE to restore old behaviour.

• more detailed output of callLOH

• renamed num.snps.segment to num.snps in callAlterations output

BUGFIXES

• fixed crash in PureCN.R when gene symbols are missing from interval file

• fixed crash in runAbsoluteCN with matched normals and high test.purity minimum (#74)

qckitfastq

                   Changes in version 0.99.12                       

• Addressed Bioconductor review points in: https://github.com/Bioconductor/Contributions/issues/753

• Added adapter content tabulation and plot implementation using RSeqAn and Rcpp

• Added checking for gzipped files (as opposed to raw fastqs) and automatic detection of quality score encoding (Sanger, Solexa, Illumina1.3, and Illumina1.5).

                   Changes in version 0.99.0                        
  

• First release

qPLEXanalyzer

                    Changes in version 1.1.4                        

• Fixed bug in coveragePlot - github Issue 15: Previously the function cleaned the beginning of each peptide sequence by gsub(“^\[.\].([A-Z]+).\[.\]$”, “\1”, .). However, it is not always the case that the terminal amino acids are surround by square brackets. I have put a more general regex in place that removes everything up to the first ‘.’ and everything after the last ‘.’.

                    Changes in version 1.1.3                        
  

• ‘ImmunoOncology’ added to BiocViews.

                    Changes in version 1.1.2                        
  

• Updates to vignette to avoid build errors when attempting to connect to Uniprot

                    Changes in version 1.1.1                        
  

• Fixed bug in maVolPlot - github Issue 12: Previously the ‘selectedGenes’ argument used GeneSymbols to match genes to highlight in the plot. Not all accessions are annotated with a GeneSymbol, and some GeneSymbols are linked to more than one Accession. This could lead to situations where incorrect genes were being highlighted due to duplicate entries or NAs. The function now accepts and matches to accessions instead - this is now noted in the man pages.

• Fixed bug in convertToMSnset - github Issue 11: The function previously threw and error if the metadata was a tibble as it needs to set row names. The function now tranforms the metadata object to a data frame.

                    Changes in version 1.1.0                        
  

• First Bioconductor Devel (Bioconductor 3.9)

qsmooth

            Changes in version 0.99.11 (2019-04-09)                 

• Fixed bug YAML in vignette causing an error on bioc nightly builds

            Changes in version 0.99.10 (2019-04-04)                 
  

• Fixed typo in ORCID

             Changes in version 0.99.9 (2019-04-04)                 
  

• Adding ORCID for Stephanie Hicks, Hector Corrada Bravo and Rafael Irizarry

             Changes in version 0.99.8 (2019-04-03)                 
  

• Fixed header of vignette .Rmd

             Changes in version 0.99.7 (2019-03-31)                 
  

• Updating usage examples in qsmooth.R so R CMD check runs under 5 mins

             Changes in version 0.99.6 (2019-03-30)                 
  

• Reducing vignette so R CMD check runs under 5 mins

             Changes in version 0.99.5 (2019-03-30)                 
  

• Updating usage examples so R CMD check runs under 5 mins

             Changes in version 0.99.4 (2019-03-29)                 
  

• Running R CMD BiocCheck gave me a warning unless I used R version 3.7, but then this failed to pass in qsmooth version 0.99.3. So back to R version 3.6

             Changes in version 0.99.3 (2019-03-29)                 
  

• Created a show method to show only first and last three values in the qsmoothWeights function and the head of the qsmoothData normalized matrix

• Updated all the examples and vignette to use the ExperimentHub bodymapRat data package

• Updated documentation in the plots.R file

• Included argument checking in the qsmooth.R file. Now checks if object is a matrix, data.frame or SummarizedExperiment.

• Included functionality for a user providing a SummarizedExperiment and extracting the counts from the assay slot (if it exists).

             Changes in version 0.99.2 (2019-03-29)                 
  

• Removed hard-coded date in DESCRIPTION file

• Included Bioconductor installation instructions in README.md file

• Changed the name of the vignette so user can use vigentte("qsmooth")

• man. Changed the description of the return to reflect the actual output

             Changes in version 0.99.0 (2019-02-07)                 
  

• Submitted to Bioconductor

QuasR

                   Changes in version 1.24.0                        

NEW FEATURES

• added support for spliced alignments using HISAT2 (via Rhisat2 package)

• migrated from Rsamtools to Rhtslib C library for operations on bam files

• migrated unit test from RUnit to testthat

• ignore reference deletions (BAM_CDEL) in qCount(…, reportLevel = “junction”)

r3Cseq

             Changes in version 1.29.0 (2018-12-08)                 

• migrated all codes to support the BioC3.9! This is because the BioC3.9 will not anymore support the ‘RangedData’ which is mainly used by r3Cseq in the previous versions.

Rbowtie

                   Changes in version 1.23.2                        

NEW FEATURES

• updated bowtie to version 1.2.2.p1 + fixes from github (up to master branch commit 58c6ac9 from Sep 5, 2018, and unmerged pull request #74)

RcisTarget

                     Changes in version 1.3                         

• Added function: getMotifAnnotation

RCM

                    Changes in version 0.3.0                        

• Importance parameters ψ are enabled again when non-parametric response functions are used, but not used for plotting.

• 2D sample plots for constrained ordination with non-parametric response functions have been disabled, as they are not interpretable. Variable plots are the only 2D plots still allowed

• Explained deviance and inertia can be plotted on the axes rahter than the ψ’s using the “plotPsi” argument to the plot.RCM() function.

• Possibility to provide lower dimensional fits has been disabled. RCM is fast enough to fit the whole model.

                    Changes in version 0.2.0                        
  

• Importance parameters ψ are no longer calculated when non-parametric response functions are used.

Rcpi

             Changes in version 1.19.2 (2019-02-24)                 

Bug Fixes

• Fixed the issues in calcTwoProtGOSim() and calcParProtGOSim() to use the latest GOSemSim API for computing GO based semantic similarity.

             Changes in version 1.19.1 (2018-11-21)                 
  

Bug Fixes

• Fixed API endpoints that are not working due to their changes across time (#5). - Fixed the vignette example for QSRR study (#6).

Improvements

• Reformat vignette code with tidyverse style.

RcwlPipelines

            Changes in version 0.99.11 (2019-03-27)                 

• 10 more tools were added.

            Changes in version 0.99.10 (2019-03-27)                 
  

• Submitted to Bioconductor

• 27 tools were collected.

RCy3

                    Changes in version 2.4.0                        

• New style setting functions - setEdgeFontFaceDefault - setEdgeFontFaceMapping - setEdgeFontSizeMapping - setEdgeLabelDefault
  • setEdgeLabelColorDefault - setEdgeLabelColorMapping - setEdgeLabelOpacityDefault - setEdgeLabelOpacityMapping - setEdgeOpacityDefault - setEdgeSourceArrowShapeMapping - setEdgeTargetArrowShapeMapping - setEdgeTooltipDefault - setNodeBorderOpacityDefault - setNodeBorderOpacityMapping - setNodeFillOpacityDefault - setNodeFillOpacityMapping - setNodeFontFaceDefault - setNodeFontFaceBypass - setNodeFontFaceMapping - setNodeFontSizeMapping - setNodeHeightDefault - setNodeHeightMapping - setNodeLabelDefault - setNodeLabelColorMapping - setNodeLabelOpacityDefault - setNodeLabelOpactiyMapping - setNodeTooltipDefault - setNodeTooltipBypass - setNodeWidthDefault - setNodeWidthMapping

• Bug Fixes - createSubnetwork – #43 network suids i/o names - openSession works with current working directory – #50 +Doc Fixes - improved visual.prop handling in mapVisualProperty – #49,#53 user report - added file overwrite warnings to all export and save functions

                    Changes in version 2.2.7                        
  

• Doc Fixes - vignette for phylogenetic trees

                    Changes in version 2.2.6                        
  

• Bug Fixes - saveSession, exportXXX – #39 default to working directory - createNetworkFromDataFrame and .edgeNameToSuids – #41 multigraph support - BiocCheck errors and warnings – #42

• Doc Fixes - added tests for multigraphs

                    Changes in version 2.2.5                        
  

• Bug Fixes - createXXXFilter and applyFilter – #40 network arg

• Doc Fixes - new filters vignette

                    Changes in version 2.2.4                        
  

• Doc Fixes - vignettes

                    Changes in version 2.2.3                        
  

• Doc Fixes - vignettes

                    Changes in version 2.2.2                        
  

• Doc Fixes - new custom graphics vignette

                    Changes in version 2.2.1                        
  

• Doc Fixes - vignettes, readme and test

recount

                    Changes in version 1.9.7                        

SIGNIFICANT USER-VISIBLE CHANGES

• Cleaned up the documentation of add_metadata() and changed the default source from recount_brain_v1 to recount_brain_v2.

                    Changes in version 1.9.6                        
  

NEW FEATURES

• citation(‘recount’)[5] now lists the recount-brain bioRxiv pre-print citation information.

                    Changes in version 1.9.5                        
  

NEW FEATURES

• We have now released the FANTOM-CAT/recount2 RSE files which you can access now through download_study(type = ‘rse-fc’). See Luidy-Imada E, Sanchez DF, et al, bioRxiv, 2019 for more information.

                    Changes in version 1.9.4                        
  

BUG FIXES

• I made the example code for geo_characteristics() more robust since currently rentrez can occasionally fails.

                    Changes in version 1.9.3                        
  

NEW FEATURES

• Add ORCID’s following changes at http://bioconductor.org/developers/package-guidelines/#description

                    Changes in version 1.9.2                        
  

BUG FIXES

• Added the argument async to snaptron_query() which can be set to FALSE to address the issue reported at https://github.com/ChristopherWilks/snaptron/issues/11

regionReport

                   Changes in version 1.17.2                        

NEW FEATURES

• Add ORCID’s following changes at http://bioconductor.org/developers/package-guidelines/#description

RepViz

                   Changes in version 0.99.14                       

RELEASE

• Implementation of the last comments from reviewers

rGREAT

                   Changes in version 1.15.1                        

• plotRegionGeneAssociationGraphs(): fixe a bug of wrong value of par(mfrow).

• fixed warnings of Rd files.

rgsepd

                    Changes in version 1.15                         

• new legends in scatterplots.

• custom point colors in PCA plot function. uses sampleMeta$CustomColor and disables the built in legend.

• custom genes in plots. See ExtractProjection() very useful, not yet in vignette - it calculates a projection among your custom gene set.

• Add lfcThreshold to the DESeq routines, so the p-values are adjusted correctly. ( implemented 1.15.1 ) This changes the behavior of most of the system. Expect a different gene set.

• New option to INIT() called renormalize, allowing user to specify preferred matrix normalization schema rather than the default DESeq2::varianceStabilizingTransform (when renormalize=FALSE).

• uses p.adjust(method=’BH’) on GOSeq’s results to shorten the GO term list. use the ‘padj’ column.

• New option to DESeq , vst with blind=TRUE/FALSE at user discretion.

• added CITATION FILE in 1.15.13

• tweaking vignette in 1.15.15 to debug bioconductor OSX build-server LaTeX versions. And 1.15.16, switching from biblatex to natbib.

rhdf5

                   Changes in version 2.28.0                        

NEW FEATURES

• Functions to test and set file locking have added. These can help identify and address problems on Lustre and ZFS file systems.

USER VISIBLE CHANGES

• Reading a dataset of rank one will now return an R vector, rather than a one dimensional array.

BUG FIXES

• Large improvements to performances when selecting subsets of datasets using the index argument.

• Resolved limitations where large datasets would exceed HDF5’s 4GB maximum chunk size. The default options will now check if this will occur and adjust chunking automatically.

• Single-rank datasets larger than 2^31-1 entries can now be read into R vectors.

Rhisat2

                   Changes in version 0.99.0                        

• Initial version

Rhtslib

                   Changes in version 1.16.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Include various additional files from Samtools 1.7: bam_aux.c, bam_endian.h, and bam_cat.c

• Add C function faidx_fetch_seq_forced_lower() to the HTSlib code. This is an alternative to HTSlib C function faidx_fetch_seq(), with the following difference: if coordinates are outside the actual sequence, write N’s, rather than adjusting the start,end. Used in the seqbias package (and originally written by seqbias’ author and maintainer, Daniel Jones).

BUG FIXES

• Fix long-standing kvsprintf() bug on Windows. This low-level bug was responsible for breaking “scan_bcf_header” .Call entry point in Rsamtools, which in turn was responsible for the infamous ‘invalid class “VCFHeader” object’ bug in VariantAnnotation::readVcf().

• Fix for Solaris: Do not build standalone executables (e.g. bgzip, tabix, etc…). They’re not needed and seem to cause problems on Solaris.

RMassBank

                   Changes in version 2.11.2                        

• Avoid writing out empty PUBLICATIONS

                   Changes in version 2.11.1                        
  

• Fix error in workflow steps 2 and 7 with rcdk >= 3.4.9

rmelting

                   Changes in version 0.99.7                        

• Fixed missing value in withWE.

                   Changes in version 0.99.6                        
  

• Removed vignette build products from git repository. - Updated installation instructions. - Fixed all instances of stop(paste(…)). - Added stringsAsFactors = FALSE to the eopts data frame. - Expanded the nested functions in meltingBatch. - Updated error and/or warning(s) handling by implementing internal function withWE. - Fixed issue with single sequence input in meltingBatch.

                   Changes in version 0.99.5                        
  

• For first review. - Changed R and rjava dependency.

                   Changes in version 0.99.4                        
  

• Converted T/F to TRUE/FALSE. - Documented return for melting.

                   Changes in version 0.99.3                        
  

• Fixed minor BiocCheck warnings. - Subscribed to mailing list.

• Fixed gitignore issue

                   Changes in version 0.99.2                        
  

• Fixed missing Tables.xlsx

                   Changes in version 0.99.1                        
  

• First BioC submission

RNASeqR

                    Changes in version 1.1.3                        

• Resolve all version bumps; Add new biocView tag “ImmunoOncology” <2018-12-4 Thu>

                    Changes in version 1.0.2                        
  

• Add new biocView tag “ImmunoOncology” <2018-12-3 Thu>

                    Changes in version 1.0.1                        
  

• Update RNASeqR.Rmd. <2018-12-3 Thu>

RnaSeqSampleSize

             Changes in version 1.15.1 (2018-11-12)                 

BUG FIXES

• Fix a bug in power estiamtion (cumsumBorder.cpp), which make results incorrect when k not equal to one.

RnBeads

                    Changes in version 2.1.2                        

• Fix in as.RnBeadRawSet

• Added new paper to CITATION

                    Changes in version 2.1.1                        
  

• Added support for SLURM compute cluster architecture

rols

                    Changes in version 2.11                         

CHANGES IN VERSION 2.11.2

• Fix failing test <2019-04-16 Tue>

CHANGES IN VERSION 2.11.1

• Add ImmunoOncology biocView

CHANGES IN VERSION 2.11.0

• New version for Bioc 3.9 (devel)

ropls

                   Changes in version 1.15.26                       

NEW FEATURE

• plot method: dev.new() is not called internally any more; consequently the ‘parDevNewL’ argument has been removed; layout can be either 1x1 or 2x2, depending on the length of the ‘typeVc’ argument; ‘fig.pdfC’ and ‘info.txtC’ arguments have been added for compatibility reasons with other packages; they have the same role as ‘file.pdfC’ and ‘.sinkC’ which now generate a deprecated warning.

                   Changes in version 1.15.24                       
  

MINOR MODIFICATION

• plot method: turning off ellipse display in case of a single sample the class

                   Changes in version 1.15.22                       
  

INTERNAL MODIFICATION

• imageF function: minor modification of the log parameter

                   Changes in version 1.15.20                       
  

NEW FEATURE

• imageF function to visualize a numerical matrix

                   Changes in version 1.15.18                       
  

INTERNAL MODIFICATION

• minor internal modification

                   Changes in version 1.15.16                       
  

INTERNAL MODIFICATION

• modification of the way additional columns are added to the pData and fData of an ExpressionSet instance

• ‘Biobase’ package now as ‘depends’ (not ‘import’)

                   Changes in version 1.15.14                       
  

INTERNAL MODIFICATION

• minor internal modification

                   Changes in version 1.15.12                       
  

INTERNAL MODIFICATION

• minor modification in examples defining ExpressionSet instances

                   Changes in version 1.15.10                       
  

INTERNAL MODIFICATION

• ‘eset’ is now a slot of the ‘opls’ class (used when the ‘opls’ method is applied to an ExpressionSet instance)

                   Changes in version 1.15.8                        
  

NEW FEATURE

• ‘plot’ method: parPaletteVc argument to specify colors

                   Changes in version 1.15.6                        
  

NEW FEATURE

• Application to ExpressionSet: first 2 scores and loadings, as well as fitted values and VIP now returned in the pData and fData

INTERNAL MODIFICATION

• Unit testing switched from ‘RUnit’ to ‘testthat’

                   Changes in version 1.15.4                        
  

INTERNAL MODIFICATION

• Checking that the data matrix does not contain any infinite or NaN value

                   Changes in version 1.15.2                        
  

INTERNAL MODIFICATION

• ImmunoOncology tag added to biocViews

• minor correction in the diagnostics graph labeling

rpx

                    Changes in version 1.19                         

rpx 1.19.4

• Delete plain NEWS now that R supports NEWS.md

rpx 1.19.3

• Fix NEWS

rpx 1.19.2

• Mention setting method on Windows <2019-04-16 Tue>

rpx 1.19.1

• Add ImmunoOncology biocView

rpx 1.19.0

• New release for Bioc 3.9

Rsamtools

                     Changes in version 2.0                         

SIGNIFICANT USER-VISIBLE CHANGES

• Migrate Rsamtools to Rhtslib. See Rsamtools/migration_notes.md for more information about this migration.

• Remove unused fields from BamRangeIterator

• Remove BAM header hash init for pileup (already memoized in Rhtslib)

RSeqAn

                    Changes in version 1.3.1                        

• CharString as/wrap wrappers and tests written.

Rsubread

                   Changes in version 1.34.0                        

• New functions: simReads() and scanFasta(). simReads() generates simulation RNA-seq reads for transcripts.

• align() and subjunc() estimate fragment length from mapped read pairs and use the estimated length to assist reporting the best alignment.

• align() and subjunc() prefer alignments with no indels included over indel-containing alignments when same number of matched bases are found.

• align() and subjunc() check if index files were successfully loaded before starting read mapping.

• align() and subjunc() detect indels arising from incorrect shifting of seed sequence when being mapped to low-complexity region and exclude such indels from read re-alignment and indel reporting.

• buildindex(), align() and subjunc() support gzipped FASTA format.

• featureCounts() allows mapped reads to have ‘*’ as their chromosome name.

• removeDupReads() supports BAM-format input and output.

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.

rWikiPathways

                    Changes in version 1.4.0                        

• Bug fixes - Fixed createSubnetwork – #43 network suids i/o names

• Doc fixes - Fixed sign in subsetting function in vignette – user issue on bioc forum - Added XML to Imports - Added the missing References section to one of the vignettes - Added BioSchemas annotation to the vignettes

S4Vectors

                   Changes in version 0.22.0                        

NEW FEATURES

• Add recursive argument to expand() methods

• Support DataFrame (or any tabular object) in Pairs

• List derivatives now support x[i] <- NULL

• Some Vector derivatives now support appending with [<-

BUG FIXES

• [<-,DataFrame only makes rownames for new rows when rownames present

• DataFrame() lazily deparses arguments

scAlign

             Changes in version 0.99.0 (2019-02-05)                 

• Submitted to Bioconductor

scater

                   Changes in version 1.12.0                        

• Removed all functions deprecated in the last release.

• Added option in runTSNE() to perform an external nearest neighbors check with BiocNeighbors. Removed the deprecated rand.seed= argument.

• Added text_by= and related options to plotReducedDim(), to overlay annotation labels onto the plot.

• Switched to BSPARAM= from BiocSingular for controlling SVD parameters. Deprecated the approximate= argument for runPCA().

• Switched runUMAP() to use uwot::umap. Added support for supplying a pre-defined set of nearest neighbors.

scds

             Changes in version 0.99.4 (2019-03-21)                 

• Added NEWS file

• Expanded readme

• Expanded vignette

scMerge

                    Changes in version 0.99                         

scMerge 0.99.24

• Updated ciation information due to PNAS acceptance.

scMerge 0.99.23

• Fixed assignment based on feedbacks

scMerge 0.99.21

• Increase code coverage to 85%.

scMerge 0.99.20

• Updated vignette on SEGs and manuals

scMerge 0.99.19

• Fixed spelling - Added verbose option - Code coverage at 75 percent (more tests on error handling needed)

scMerge 0.99.17

• Fixed README install_github vignette issue. - Fixed pkgdown organisation issue. - Major updates on the scReplicate function: more informative messages. - Using cross-product of matrix to perform SVD to speed up calculations. - Added testing scripts. - Fixed vignette text output issues.

scMerge 0.99.11

• Reduced data size in scMerge to pass BioC checks

scran

                   Changes in version 1.12.0                        

• Added option in quickCluster() to cluster on log-expression profiles. Modified defaults to use graph-based clustering on log-expression-derived PCs.

• Modified default choice of ref.clust= in computeSumFactors(). Degrade quietly to library size factors when cluster is to small for all pool sizes.

• Minor change to cyclone() random number generation for consistency upon parallelization.

• Added BPPARAM= to correlateNull() for parallelization. Minor change in random number generation for consistency upon parallelization.

• Minor change to parallelPCA() random number generation for consistency upon parallelization.

• Created correlateGenes() function to compute per-gene correlation statistics.

• Modified correlatePairs() to compute expected rho after all possible tie-breaking permutations. Deprecated cache.size= as all ranks are now returned as in-memory representations. Deprecated per.gene= in favour of an external call to correlateGenes(). Deprecated tol= as ties are now directly determined by rowRanks().

• Switched to BiocSingular for PCA calculations across all functions. Deprecated approximate= and pc.approx= arguments in favour of BSPARAM=.

• Deprecated all batch correction functions to prepare for the migration to batchelor.

scRecover

             Changes in version 1.0.0 (2019-05-01)                  

• Package released

            Changes in version 0.99.15 (2019-04-20)                 
  

• Correct parallelization in scImpute (imputation_model.R)

• Resume use set.seed in scImpute (imputation_model.R)

• Update vignettes

            Changes in version 0.99.10 (2019-04-03)                 
  

• Add Unit Tests to functions

• Update vignettes

• Made the following significant changes o Change default outputDir to temporary directory o Add parameter verbose to scRecover function

             Changes in version 0.99.0 (2019-02-21)                 
  

• Submitted to Bioconductor

             Changes in version 0.1.0 (2018-05-30)                  
  

• Package created

scTensor

                   Changes in version 0.99.22                       

• newCCSParams, getParam, setParam, and cellCellSimulate are added

• The hyperlinks to CMap (Connectivity Map) are embedded in the HTML report

                   Changes in version 0.99.21                       
  

• Some bugs are fixed

                   Changes in version 0.99.18                       
  

• Enrichment Analysis is added in cellCellReport()

                   Changes in version 0.99.15                       
  

• Accepted in BioC 3.9

                   Changes in version 0.99.6                        
  

• Revised and modified some parts

                   Changes in version 0.99.0                        
  

• Package released

seq2pathway

                   Changes in version 1.15.0                        

• Added function plotTop10

SeqArray

                   Changes in version 1.24.0                        

NEW FEATURES

• a new function seqResetVariantID()

• a new option in seqRecompress(, compress="none") to uncompress all data

• seqGetData() allows a GDS file name in the first argument

                Changes in version 1.22.4-1.22.6                    
  

BUG FIXES

• seqSetFilter(, sample.id=) fails to correctly select samples in rare cases (since SeqArray>=v1.22.0 uses the distribution of selected samples to optimize the data access of genotypes, see https://github.com/zhengxwen/SeqArray/issues/48)

• the bgzf VCF file is truncated in seqGDS2VCF() since the file is not closed appropriately

• invalid chromosomes and position in the output of seqMerge() when merging different samples but same variants

                Changes in version 1.22.1-1.22.3                    
  

UTILITIES

• more information in seqDelete()

NEW FEATURES

• a new option ‘scenario’ in seqVCF2GDS() and seqBCF2GDS()

BUG FIXES

• export a haploid VCF file using seqGDS2VCF()

• export VCF without any FORMAT data in seqGDS2VCF()

• export GDS without genotypes in seqExport()

• fix parallel file writing in seqVCF2GDS(), when no genotype

seqCAT

                    Changes in version 1.6.0                        

FEATURES

• Make the variant caller-specific filtering optional (on by default) and rename the relevant parameter names for increased clarity

• Add a check to look for gVCF files as input, including the existance of <NON_REF> alleles (common for gVCF files)

• Add checks to see if input VCFs correctly contain DP, AD and GT data

seqcombo

                    Changes in version 1.5.1                        

• fixed R check by import dplyr::n (2019-01-02, Wed)

SeqVarTools

                   Changes in version 1.21.5                        

• getGenotype and getGenotypeAlleles work for haploid genotypes.

                   Changes in version 1.21.4                        
  

• Add vignette describing iterators.

                   Changes in version 1.21.1                        
  

• Add method to return imputed dosage.

sevenbridges

                   Changes in version 1.13.5                        

Improvements

• Added new platform options for the recently introduced environments. Now we can choose from “aws-us”, “aws-eu”, “ali-cn”, “cgc”, “cavatica”, and “f4c” in Auth() calls.

                   Changes in version 1.13.4                        
  

New Features

• Added support for Markers API (Advance Access feature). See the Markers API section in the vignette for details. - Added support for Actions API. See the Actions API section in the vignette for details.

Improvements

• Added a new field description to the Files class following the recent API improvements. - Updated the API vignette to reflect the platform default setting update for spot instances (spot is now enabled by default).

                   Changes in version 1.13.3                        
  

New Features

• Added support for Enterprise API. See the Enterprise API section in the vignette for details.

Improvements

• Removed unnecessary package dependencies to optimize the time needed for package installation and loading. - New look for the documentation website with improved text readability.

                   Changes in version 1.13.2                        
  

New Features

• Added support for Folder API. See the Folders API section in the vignette for details.

Improvements

• Added floating TOC and changed the vignette theme for the HTML vignettes available on Bioconductor, to improve the browsing experience for long vignettes.

Bug Fixes

• Fixed Docker image build issue and updated Bunny version.

                   Changes in version 1.13.1                        
  

New Features

• Added support for setting execution hints per task run when drafting new tasks.

signeR

                    Changes in version 1.9.3                        

• fix parsing issue in genCountMatrixFromVcf for some vcfs

                    Changes in version 1.9.2                        
  

• fix for genCountMatrixFromVcf fails with phased genotypes

• added one-vcf-per-sample example to vignette

                    Changes in version 1.9.1                        
  

• fix prototype mismatch issue

• fix plot error: non-finite ylim when pvalue=0

singscore

                    Changes in version 1.3.2                        

• allow continous and discrete annotations for plotDispersion and projectScoreLandscape. Annotations can now be part of the score data.frame and then specified as a column name - plot themes updated

• citation updated: cite the singscore manuscript - number of bins for the hexbin plot in plotLandscape is determined from the data - fixed bug in calculation of scores. Boundary calculation was previously done with all genes in the gene-set. It should be done with genes present in both the gene-set and the data (i.e. after filtering out those not measured in the data). - TotalDispersion now estimated as the mean of dispersions from the up- and down-regulated gene sets instead of the sum (previous estimate divided by 2)

                    Changes in version 1.2.2                        
  

• created a website for the package - added ORCID IDs for authors - added sticker for package

sitePath

                   Changes in version 0.99.28                       

• Bug fix: Internal indexing error in ‘multiFixationSites’

• The default for ‘makePlot’ in ‘sneakPeak’ changed to False

• The default ‘tolerance’ in ‘fixationSite’ changed to 0.01

• Improve visualization of ‘fixationSites’ return

                   Changes in version 0.99.27                       
  

• Improve ‘multiFixationSite’ with a two-way greedy algorithm

• Use dash line for excluded ‘lineagePath’ in ‘plotSingleSite’

                   Changes in version 0.99.26                       
  

• Bug fix: ‘nodeAAsum’ subscript out of bound in ‘multiFixationSite’

                   Changes in version 0.99.25                       
  

• Use amino acid color for ‘plotSingleSite.fixationSite’

• Add ‘excluded’ legend to ‘plotSingleSite’

• Update DESCRIPTION and NEWS

• Use BiocStyle for vignettes

                   Changes in version 0.99.6                        
  

• New functionality ‘multiFixationSites’

• Rewrite pruner functions

• Add ‘minPath’ argument for ‘sneakPeek’

• ‘sitePath’ function’s name changed to ‘lineagePath’

• Minimum entropy

• The underlying data structure

                   Changes in version 0.99.5                        
  

• Add new functionality ‘addMSA’

• Avoid ‘root.phylo’ function

SNPRelate

                   Changes in version 1.18.0                        

• snpgdsBED2GDS() allows a single file name without the extended file names (.bed, .fam, .bim)

SpatialCPie

             Changes in version 1.0.0 (2018-08-17)                  

• Initial release

specL

            Changes in version 1.17.22 (2019-01-24)                 

• code cosmetics to eliminate ERRORS and WARNINGS in R CMD BiocCheck of version 3.9.

splatter

             Changes in version 1.8.0 (2018-04-18)                  

• Add a Splat parameters vignette

• Rename the Splat path.length parameter to path.nSteps

• Fix a bug with parameter order in setParams

• Fix a bug where Splat groups were being simulated in alphanumeric order

• Protect against integer overflow in simulation functions

sRACIPE

             Changes in version 0.99.0 (2019-04-01)                 

• submitted to Bioconductor

ssrch

                   Changes in version 0.99.0                        

• added to Bioconductor 3.9

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 1.13.7                        
  

• Results of Volcano plot (add the log2(FC) and -log10(p.adjust) values)

Structstrings

             Changes in version 0.99.0 (2019-03-01)                 

• Submitted to Bioconductor

StructuralVariantAnnotation

             Changes in version 0.99.0 (2019-04-05)                 

• Submitted to BioConductor

SWATH2stats

                   Changes in version 1.13.6                        

UPDATE

• aLFQ is deprecated on CRAN and thus Vignette cannot depend anymore on the aLFQ package.

                   Changes in version 1.13.5                        
  

NEW FEATURES

• Update plot_variation and plot_variation_vs_total function

                   Changes in version 1.13.4                        
  

NEW FEATURES

• Update version for JPP (new version of pyprophet)

                   Changes in version 1.13.3                        
  

UPDATE

• DESCRIPTION: move PECA to enhances

                   Changes in version 1.13.2                        
  

UPDATE

• Vignette: make PECA chunk eval=FALSE to prevent error when the PECA package is not available on BioC

                   Changes in version 1.13.1                        
  

NEW FEATURES

• Add ImmunoOncology to biocViews

                   Changes in version 1.13.0                        
  

NEW FEATURES

• SWATH2stats in BioC 3.9 development release

SynMut

            Changes in version 0.99.12 (2019-04-29)                 

• Important bug fix in function “dinu_to”: fixed wrong result in sample methods.

            Changes in version 0.99.11 (2019-04-29)                 
  

• Important bug fix in function “get_du”: fixed the step parameter in oligonucleotideFrequency.

            Changes in version 0.99.10 (2019-04-23)                 
  

• Update documents.

             Changes in version 0.99.9 (2019-04-23)                 
  

• Reduced dependency on seqinr.

             Changes in version 0.99.8 (2019-04-23)                 
  

• Updated DESCRIPTION.

             Changes in version 0.99.7 (2019-04-23)                 
  

• Updated NAMESPACE.

             Changes in version 0.99.6 (2019-04-23)                 
  

• Updated the Bioconductor installation instructions in readme and vignette.

             Changes in version 0.99.5 (2019-04-23)                 
  

• Added bioconductor installation instructions to README and vignette.

• Added comments to vignette to make workflow more clear.

• Duplicated code in the following functions were converted to helper functions. o codon_random.R o codon_to.R o dinu_to.R o codon_mimic.R

• Added region_related.R to store the helper functions related to extracting or merging region.

• Eliminated 67 lines of duplicated code in dinu_to.R

• Eliminated duplicated code in input_seq.R

             Changes in version 0.99.0 (2019-04-16)                 
  

• Submitted to Bioconductor

TargetSearch

                   Changes in version 1.40.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• The graphical user interface (TargetSearchGUI) is being deprecated. This is due to old source code, lack of time for maintenance, and lack of interest. The GUI it is still part of this release and it will be removed in the next release, ie, 1.42.0

BUG FIXES

• Fix NA handling in quantMass method.

TCGAbiolinks

                   Changes in version 2.11.2                        

• Add GISTIC2 case to GDC prepare and manuals

TFEA.ChIP

                    Changes in version 1.3.5                        

New Features

• Integrate enrichment analysis results by TF with rankTFs(). The function uses the output of getCMstats() to perform Wilcoxon rank-sum test or GSEA on the ChIPs ordered by distance score.

New default database

• The TF-Gene database included with TFEA.ChIP was built using ReMap’s ChIP-seq collection (v. 2018) and GeneHancer’s Double Elite regulatory regions (v. 4.8). Because of memory limits, the internal database included in TFEA.ChIP only stores ChIP-gene information from the 1060 ChIP-seqs from the ENCODE project included in ReMap 2018. To download the full database, as well as other ready-to-use databases generated for TFEA.ChIP, visit: https://github.com/LauraPS1/TFEA.ChIP_downloads

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()

topconfects

             Changes in version 1.1.4 (2018-12-29)                  

• Prepare for Bioconductor submission.

             Changes in version 1.1.3 (2018-11-14)                  
  

• Add “full” output option for limma_confects and normal_confects, which adds se, df, and fdr_zero columns.

             Changes in version 1.1.2 (2018-06-30)                  
  

• Add DESeq2 support.

• Code to do with non-linear effect sizes has been move to the “ql” branch on github, pending publication of the basic method and a possible rethink and use of a simpler method.

             Changes in version 1.0.1 (2018-02-04)                  
  

• Initial release.

             Changes in version 0.99.5 (2019-02-18)                 
  

• Include a vignette giving an overview of the package’s functions.

             Changes in version 0.99.4 (2019-02-06)                 
  

• Reduce build time of vignette.

             Changes in version 0.99.3 (2019-02-05)                 
  

• Where :: is used, use requireNamespace first to give an informative error message.

• Use match.arg in edger_confects.

• More tests.

             Changes in version 0.99.2 (2019-01-15)                 
  

• Version bumped to test web-hook and Bioconductor automated build system.

             Changes in version 0.99.1 (2018-12-30)                 
  

• Switch to required version number for Bioconductor submission.

• Switch email to address subscribed to bioc-devel.

• Require R 3.6.

topdownr

                     Changes in version 1.5                         

• New version for Bioc 3.9 (devel)

Changes in version 1.5.6

• Revert changes for NULL indices of DataFrame introduced in 1.5.4 (a419f59, c4bfc1c) because they are fixed upstream in S4Vectors. Keep unit tests in place. [2019-03-27]

Changes in version 1.5.5

• Depends on R >= 3.5.0 now, because the seralization format changed in R.

Changes in version 1.5.4

• Fix for internal .makeRowNames/.colsToLogical/.colsToRle on DataFrame without any numeric/character columns. - Fix unit test that uses set.seed (order changed during R-devel upgrade).

Changes in version 1.5.3

• biocViews: ImmunoOncology added by Kayla-Morrell kayla.morrell@roswellpark.org [2019-01-04].

Changes in version 1.5.2

• Add expandMs1Conditions, expandTms2Conditions, createExperimentsFragmentOptimisation functions to allow more flexibility in method creation; see also #77 [2018-12-07]. - Modify interface/arguments of writeMethodXmls to adapt to new method creation workflow (the old interface will be defunct in Bioconductor 3.10 and removed in 3.11) [2018-12-07]. - Adapt the data-generation vignette to the new workflow [2018-12-07]. - Deprecated defaultMs1Settings and defaultMs2Settings. They will be defunct in Bioconductor 3.10 and removed in 3.11 [2018-12-07].

Changes in version 1.5.1

• readTopDownFiles gains the argument conditions to control wheter “FilterStrings” or a given number of conditions is used to create condition IDs; see #77 [2018-11-07].

TPP2D

             Changes in version 0.99.0 (2019-03-12)                 

• Submitted to Bioconductor

trackViewer

                   Changes in version 1.19.28                       

• fit the small size canvas.

                   Changes in version 1.19.27                       
  

• add safe color theme.

                   Changes in version 1.19.26                       
  

• update author info.

                   Changes in version 1.19.25                       
  

• change save and load name for browseTracks.

                   Changes in version 1.19.24                       
  

• add save and load for browseTracks.

• add swith dandelion height method (mean or count) for browseTracks.

                   Changes in version 1.19.23                       
  

• add color picker for pie.stack for browseTracks.

                   Changes in version 1.19.22                       
  

• fix the bug in legend for browseTracks.

                   Changes in version 1.19.21                       
  

• fix the bug of that can not set color for undefined for browseTracks.

                   Changes in version 1.19.20                       
  

• fix the bug of lable is not saved for browseTracks.

                   Changes in version 1.19.19                       
  

• fix the bug of output svg for browseTracks.

                   Changes in version 1.19.18                       
  

• add rotate 45 in color picker for browseTracks.

                   Changes in version 1.19.17                       
  

• add apply to all in color picker for browseTracks.

                   Changes in version 1.19.16                       
  

• fix the grammar in vignettes.

                   Changes in version 1.19.15                       
  

• update vignettes.

                   Changes in version 1.19.14                       
  

• update undo for browseTracks.

                   Changes in version 1.19.13                       
  

• add undo for browseTracks.

                   Changes in version 1.19.12                       
  

• add remove all guideline function.

                   Changes in version 1.19.11                       
  

• fix the fonts bug for export png in browseTracks

                   Changes in version 1.19.10                       
  

• remove all svgs before browseTracks

                   Changes in version 1.19.9                        
  

• Build shiny output objects for browseTracks

                   Changes in version 1.19.8                        
  

• add dandelion plots to browseTracks

                   Changes in version 1.19.7                        
  

• fix a bug in track class

• improve one-step visualization for browseTracks

                   Changes in version 1.19.6                        
  

• improve one-step visualization for browseTracks

• try to avoid the error caused by VariantAnnotation

                   Changes in version 1.19.5                        
  

• improve one-step visualization for browseTracks

                   Changes in version 1.19.4                        
  

• add one-step visualization for browseTracks

                   Changes in version 1.19.3                        
  

• adjust y label position for viewTracks

                   Changes in version 1.19.2                        
  

• adjust legent position for dandelion.plot

                   Changes in version 1.19.1                        
  

• add featureLayerID to dandelion.plot

transcriptogramer

                    Changes in version 1.5.6                        

• All datasets were updated to match data from STRINGdb release 11.

                    Changes in version 1.5.1                        
  

• Change on the differentiallyExpressed() method return: output now contains raw p-values.

• Change on the clusterEnrichment() method return: output now contains raw p-values.

• A section called “Frequently asked questions” has been added in the vignette.

transite

                    Changes in version 1.0.2                        

• updated roxygen2

• updated license

• clarified argument description of SPMA

• fixed issue with multi-threaded cluster environment

                    Changes in version 1.0.1                        
  

• fixed typo in vignette

• added code example for drawVolcanoPlot function

• increased size of circles for motif-associated k-mers in drawVolcanoPlot function

treeio

                    Changes in version 1.7.4                        

• update test according to the change of default RNG in the comming R-3.6 (2019-04-02, Tue)

                    Changes in version 1.7.3                        
  

• rescale_tree from ggtree (2019-01-11, Fri)

                    Changes in version 1.7.2                        
  

• MRCA methods for phylo and treedata (2019-01-10, Thu) - mv vignettes to treedata-book - root method from ggtree::reroot (2018-12-28, Fri) - rename to root for importing ape::root generic

                    Changes in version 1.7.1                        
  

• compatible with tibble v=2.0.0 (2018-11-29, Thu)

tRNA

             Changes in version 1.1.2 (2018-03-27)                  

• bugfix for padding unpaired region in stem sequences

• bugfix for getting empty sequences of non-existing variable loops

• fixed man page issue

             Changes in version 1.1.1 (2018-12-01)                  
  

• added Structstrings dependency

• getBasePairing now used from Structstrings package

• optimizations

tRNAdbImport

             Changes in version 1.1.1 (2019-01-26)                  

• added Modstrings and Structstrings dependency

• depending on the database selected the tRNA sequences will be returned as DNAStringSet or ModRNAStringSet

• now uses the DotBracketStringSet from the Structstrings package to store the structure information

tRNAscanImport

             Changes in version 1.3.2 (2018-02-16)                  

• now exits with error message, if empty lines as delimiter of tRNA entries is found

             Changes in version 1.3.1 (2018-01-26)                  
  

• now uses the DotBracketStringSet from the Structstrings package to store the structure information

TVTB

             Changes in version 1.9.2 (2019-02-20)                  

Bug fix

• Fixes to pass updated BiocCheck requirements.

tximeta

                   Changes in version 1.1.18                        

• Specifying gene=TRUE in addIds() when rows are transcripts will attempt to use a gene_id column to map the IDs. This usually gives a better mapping rate.

tximport

                   Changes in version 1.11.1                        

• Added argument ‘sparse’ and ‘sparseThreshold’ to allow for sparse count import. For the initial implemenation: only works for txOut=TRUE; countsFromAbundance either “no” or “scaledTPM”; doesn’t work with inferential replicates, and only imports counts (and abundances if countsFromAbundance=”scaledTPM”).

Ularcirc

                    Changes in version 1.1.3                        

NEW FEATURES

• Added ability to upload CIRI2 and circExplorer2 output

• New analysis features: PCA plot, heatmap analysis, distribution analysis

BUG FIXES

• Amended TwoSzabo dataset

• Amended workflow to minimise system crashes

Uniquorn

             Changes in version 2.3.5 (2019-02-27)                  

Fixed another windows VCF parse error

• Fixed yet another VCF file parsing error associated with the VariantAnnotation R package parser.

             Changes in version 2.3.4 (2019-02-25)                  
  

Fixed windows VCF parse error

• Uniquorn experienced an error when parsing the internal test vcf file on Windows systems.

             Changes in version 2.3.3 (2019-02-22)                  
  

Unzip test vcf file

• Unzipped the tested vcf file since VarriantAnnotion parser failed to read zipped file in future R version 3.6

             Changes in version 2.3.2 (2019-02-04)                  
  

Remove dependency

• Removed dependency on data.table

• Removed data.table import due to biocondcutor request

universalmotif

                    Changes in version 1.2.0                        

NEW FEATURES

• New motif_peaks() function: test for significantly overrepresented peaks of motif sites in a set of sequences.

• New get_bkg() function: calculate background frequencies of sequence alphabets, including higher order backgrounds. Works for any sequence alphabet. Can also create MEME background format files.

• read_meme() has a new option, readites.meta, which allows for reading individual motif site positions and P-values, as well as combined sequence P-values.

• shuffle_sequences(…, method = “markov”) works for any set of characters instead of just DNA/RNA.

• shuffle_sequences(): new shuffling method, ‘euler’. This allows for k>1 shuffling that preserves exact letter counts, as opposed to ‘markov’. This method is set as the new default shuffling method.

• create_sequences() has a new option “freqs” which allows for generating sequence from higher order backgrounds and any sequence alphabet (options “monofreqs”, “difreqs” and “trifreqs” are now deprecated).

• universalmotif objects can now hold onto higher order backgrounds.

• motif_pvalue() with use.freq > 1 can calculate P-values from provided higher-order backgrounds, instead of assuming a uniform background.

• add_multifreq() adds corresponding higher order background probabilities to motifs.

• New get_klets() utility function: generate all possible k-lets for any set of characters.

• New score_match() utility function: score a match for a particular motif.

• New get_matches() utility function: get all possible motif matches above a certain score.

• New count_klets() utility function: count all k-lets for any string of characters.

• New motif_score() utility function: calculate motif score from input thresholds.

• New shuffle_string() utility function: shuffle a string of character using one of three methods: euler, linear, and markov.

• The native write_motifs()/read_motifs() universalmotif format is now YAML based. Motifs written before v1.2.0 can still be read by read_motifs().

MINOR CHANGES

• Increased input security for character type parameters throughout.

• Expanded motif_pvalue(), scan_sequences(), motif_tree() examples sections.

• New vignette sections for motif_peaks() and get_bkg() added to SequenceSearches.Rmd.

• Various vignette tweaks.

• Fixed various spelling mistakes throughout, added Language field to Description, and added spell check to tests.

• Documentation for the “random” shuffling method has been removed and a warning is shown when used to tell the user that it will be removed in the next minor update.

• Generally increased test coverage.

• The “k=1”, “linear” and “markov” shuffling methods are much faster.

• create_sequences() for higher order backgrounds is much faster.

• Faster add_multifreqs(): slight improvement for DNA motifs, big improvement for non-DNA motifs.

• sample_sites() has been rewritten for use.freq > 1: the probability of each letter in the site is now dependent on the previous letters (also faster and more memory efficient for any use.freq).

• Improvement to calculating motif scores from p-value input: no longer guesses different scores, instead estimating a normal distribution of scores. This new approach is much, much faster and more memory efficient. It does however assume a uniform background.

• The “score.pct” column in scan_sequences() results now represents the percent score based on the total possible score, not just the score between zero and the max possible score.

• summarise_motifs() is much faster.

• Objects in data/ are saved using serialization format version 3.

• convert_motifs(motif, class = “universalmotif-universalmotif”): performs a validObject() check if “motif” is a universalmotif object.

• The show() method for universalmotif objects performs a validObject() check first.

• motif_rc() has a new option “ignore.alphabet”, used to turn on or off the alphabet check (checks for DNA/RNA motif).

• Added “overwrite” and “append” options to write_*() functions.

• enrich_motifs(…, return.scan.results = FALSE): uses a slimmed down version of scan_sequences() which skips construction of the complete results data.frame, saving a tiny bit of time on large jobs.

• compare_motifs() now includes log P-values. This way comparisons can still be properly ranked even if their P-values are below the machine limit.

• convert_motifs() from MotifList (MotifDb) carries over dataSource.

• If a MEME motif has two names, the second will be assigned as “altname” by read_meme().

• Utilities documentation has been split into two: ?utils-motif and ?utils-sequence.

BUG FIXES

• Fixed IC score calculation from character input in create_motif().

• The internal DNA consensus letter calculation previously did not assign ambiguous letters when one PPM position was >0.5 and another was >0.25. This was unintended behaviour and will now output the proper ambigous DNA letter.

variancePartition

                   Changes in version 1.13.5                        

• add plotContrasts() to dream vignette

                   Changes in version 1.13.4                        
  

• export classes to fix bug with class “varPartResults” not being defined

• Thanks Megan Behringer

                   Changes in version 1.13.3                        
  

• add plotContrasts()

                   Changes in version 1.13.2                        
  

• Enable random slope models in dream, but not for estimating variance fractions

• Thanks Jonas Zierer

                   Changes in version 1.13.1                        
  

• Add progress bar at ETA

VennDetail

            Changes in version 0.99.18 (2019-04-25)                 

• address warnings

            Changes in version 0.99.17 (2019-04-25)                 
  

• address warnings

            Changes in version 0.99.16 (2019-04-25)                 
  

• address issues

            Changes in version 0.99.15 (2019-04-23)                 
  

• rewrite the vennpie function

            Changes in version 0.99.14 (2019-04-22)                 
  

• rewrite the venndetail function

            Changes in version 0.99.13 (2019-04-20)                 
  

• update the vignette

            Changes in version 0.99.12 (2019-03-29)                 
  

• update the vignette

            Changes in version 0.99.11 (2019-03-27)                 
  

• revised function based on the comments

            Changes in version 0.99.10 (2019-02-25)                 
  

• add wide output format

             Changes in version 0.99.9 (2019-02-20)                 
  

• add wide output format

             Changes in version 0.99.8 (2019-02-10)                 
  

• fix error,warnings and notes

             Changes in version 0.99.7 (2019-02-09)                 
  

• update man doc

             Changes in version 0.99.6 (2019-02-09)                 
  

• add show as generic function

             Changes in version 0.99.5 (2019-02-08)                 
  

• update Get function

             Changes in version 0.99.4 (2019-02-07)                 
  

• update NAMESPACE

             Changes in version 0.99.3 (2019-02-07)                 
  

• modify the get function to Get

             Changes in version 0.99.2 (2019-02-07)                 
  

• revised the test function

             Changes in version 0.99.1 (2019-02-07)                 
  

• delete Rproj file

             Changes in version 0.99.0 (2019-02-05)                 
  

• Submitted to Bioconductor

xcms

                    Changes in version 3.5.5                        

• Add dirname and dirname<- methods for OnDiskMSnExp to change the path to the raw data files.

• Add section “Subset-based alignment” to the xcms vignette to describe the alignment possibility to perform alignments based on a subset of samples (e.g. QC samples).

                    Changes in version 3.5.4                        
  

• Fix problem in featureChromatograms with include = “feature_only” that could return a non-valid object.

• Ensure that XCMSnExp objects are updated if necessary in all analysis methods.

                    Changes in version 3.5.3                        
  

• Fix unit tests.

                    Changes in version 3.5.2                        
  

• Small changes in fillChromPeaks,XCMSnExp to reduce memory demand.

• Fix issue #359.

• Fix issue #360: rawEIC skipped last scan/spectrum if rtrange was provided.

• filterMsLevel keeps now chromatographic peaks and feature definitions from the specified MS levels (issue #362).

• Fix bug in xcmsRaw that leads to a netCDF error message (issue #363).

• Add parameter msLevel to chromPeaks for XCMSnExp objects.

• Add chromPeakData to allow adding arbitrary annotation to chromatographic peaks.

• Change default of parameter value in featureValues from value = “index” to value = “into”.

• Add parameter isFilledColumn to chromPeaks allowing the old behaviour to include the is_filled column in the chromatographic peak matrix.

                    Changes in version 3.5.1                        
  

• Fix issue #349.

• Add updateObject function for XCMSnExp objects (issue #347).

• Add dropFilledChromPeaks methods for XChromatogram and XChromatograms objects.

• Add parameter filled = FALSE to chromatogram and featureChromatograms functions.

• Fix matchedFilter peak detection problems with empty spectra (issue #325).

• featureChromatograms extracts by default only chromatographic peaks associated with a feature.

• chromatogram,XCMSnExp extracts an XChromatogram containing also chromatographic peaks and feature definitions.

• Add featureValues method for XChromatograms objects (issue #336).

• Add correspondence analysis (peak grouping) for chromatographic data (for now only with PeakDensity method; issue #336).

• Add featureDefinitions slot to XChromatograms object and related accessor methods.

• Add subset alignment option subsetAdjust = “average” to adjust left-out samples (blanks or simply non-subset samples) based on an interpolation from the results of the previous and subsequent subset sample.

• Add parameter subsetAdjust to PeakGroupsParam allowing to switch between different methods to adjust samples left out in the alignment process.

• Alignment based on a sample subset for the peak groups method (issue #335): sample subset can be defined with the subset parameter, samples not included in the subset will be aligned based on the adjusted retention times of the closest sample in the subset.

• Add findChromPeaks,XChromatograms (issue #332).

• Add processHistory,XChromatograms.

• Add plot,XChromatograms method with automatic peak highlighting (issue #334).

• Add hasChromPeaks,XChromatograms method.

• Add XChromatograms class with constructor function and coercing method.

• Add hasChromPeaks,XChromatogram method.

• Add filterRt,XChromatogram, filterMz,XChromatogram.

• Add plot,XChromatogram function supporting of highlighting/drawing identified chromatographic peaks.

• findChromPeaks,Chromatogram returns an XChromatogram object (issue #329).

• Add chromPeaks,XChromatogram (issue #329).

• Add XChromatogram object (issue #329).

• Fix higlightChromPeaks with type = “polygon”: peak filling represents now the full detected peak and is no longer cut by the provided rt.

• Add argument peakIds to highlightChromPeaks allowing to specify the IDs of peaks to be highlighted.

• Add example on clustering of base peak chromatograms to the vignette (issue #328).

• Small fix in the vignette (issue #327).

• Add parameter groupval to exportMetaboAnalyst (issue #296).

• Fix bug in show,XCMSnExp that would throw an error if no process history is present.

Xeva

                   Changes in version 0.99.7                        

• This is the new version

zinbwave

             Changes in version 1.5.3 (2019-04-19)                  

• Updated vignette to reflect new way of interacting with Seurat.

• Illustrate the use of approximate zinbsurf function.

             Changes in version 1.4.2 (2019-03-11)                  
  

• Fix bug in computeObservationalWeights.

NEWS from new and existing Data Experiment Packages

bodymapRat

             Changes in version 0.99.8 (2019-04-04)                 

• Adding ORCID for Stephanie Hicks

             Changes in version 0.99.7 (2019-04-03)                 
  

• Fixed error in header of vignette

• Adding citation to package

             Changes in version 0.99.6 (2019-03-29)                 
  

• Added documentation for bodymapRat object with examples

             Changes in version 0.99.5 (2019-03-27)                 
  

• Added .onLoad() function as noted in ExperimentHub documentation

• Converted vignette and unit tests to load data from ExperimentHub

             Changes in version 0.99.4 (2019-03-27)                 
  

• Now have successfully removed .rda object from data/ folder

• BFG Repo-Cleaner to remove large data file and clean git tree

             Changes in version 0.99.3 (2019-03-19)                 
  

• Convert data package to ExperimentHub package

• Removed .rda object from data/ folder

• Removed Maintainer from DESCRIPTION file

• Updated README.md to include bioconductor installation

• Moved and renamed file to create data object into inst/scripts/make-data.Rmd

• Created a make-metadata.R file

             Changes in version 0.99.1 (2019-02-23)                 
  

• Compressed and re-saved data object

             Changes in version 0.99.0 (2019-02-07)                 
  

• Submitted to Bioconductor

CluMSIDdata

                   Changes in version 0.99.5                        

• added some more data for CluMSID MTBLS vignette

                   Changes in version 0.99.4                        
  

• removed invalid character from GC_post.csv

                   Changes in version 0.99.3                        
  

• updated R version dependency to 3.6

                   Changes in version 0.99.2                        
  

• updated R version dependency to 3.5.1

                   Changes in version 0.99.1                        
  

• started ignoring CluMSIDdata.Rproj

• updated R version dependency

                   Changes in version 0.99.0                        
  

• Bioconductor submission

                    Changes in version 0.1.0                        
  

• migrated data needed for vignette and examples from CluMSID to CluMSIDdata

curatedAdipoChIP

             Changes in version 0.99.0 (2019-03-26)                 

• Submitted to Bioconductor

curatedAdipoRNA

             Changes in version 0.99.0 (2019-02-06)                 

• Submitted to Bioconductor

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.

FlowSorted.CordBloodCombined.450k

             Changes in version 0.99.0 (2019-01-21)                 

• Submitted to Bioconductor

• Added NEWS file

• Initial development release

HCAData

                    Changes in version 0.1.0                        

New features

• Initial version of the package!

HDCytoData

                    Changes in version 1.3.4                        

• Add Samusik_01, Samusik_all, Nilsson_rare, and Mosmann_rare datasets

• Add Krieg_Anti_PD_1 dataset

• Include additional information in ‘description’ slot for flowSet object for Bodenmiller_BCR_XL dataset

• Update documentation

                    Changes in version 1.3.2                        
  

• Add Levine_32dim and Levine_13dim datasets

• Include additional information in ‘description’ slot for flowSet object for Bodenmiller_BCR_XL dataset

                    Changes in version 1.3.1                        
  

• Update flowSet object for Bodenmiller_BCR_XL dataset to include raw channel names

mcsurvdata

                    Changes in version 1.0.1                        

• Package submission

MOFAdata

             Changes in version 0.99.0 (2019-01-25)                 

• Submitted to Bioconductor

mtbls2

                   Changes in version 1.13.1                        

• filePaths of raw files are now patched to match the location of the installed mtbls2 package upon onAttach(), to be compliant with the staged-install approach

NestLink

            Changes in version 0.99.96 (2019-04-24)                 

• added DOI 10.1038/s41592-019-0389-8 in citation.

            Changes in version 0.99.83 (2018-12-20)                 
  

• new Dockerfile.

• new vignette make-data.Rmd.

• use <URL: http://bioconductor.org/packages/devel/bioc/html/ExperimentHub.html>.

• moved all package data to aws s3. data are now available by using ExperimentHub.

            Changes in version 0.99.50 (2018-09-25)                 
  

• prepare for submission on bioconductor.

PtH2O2lipids

                 Changes in version 2016-04-21                      

• Initial release for Bioconductor

qPLEXdata

                    Changes in version 1.1.1                        

• Fixed broken code in Vignette

NEWS from new and existing Workflows

BgeeCall

                    Changes in version 1.0.0                        

• Public release of BgeeCall package. Enjoy!!!

recountWorkflow

                    Changes in version 1.7.2                        

BUG FIXES

• Fix the call to bumphunter::annotateTranscripts().

• See https://gist.github.com/lcolladotor/196dabeb1ac628c35656bfa94b5d9577 for more details.

                    Changes in version 1.7.1                        
  

BUG FIXES

• Fix the ftp url for the Gencode v25 gtf file.

SingscoreAMLMutations

             Changes in version 0.99.0 (2019-03-25)                 

• Submitted to Bioconductor

Deprecated and Defunct Packages

Thirteen software packages were removed from this release (after being deprecated in Bioc 3.8): nudge, GeneSelector, BiocInstaller, RamiGO, prot2D, ampliQueso, gaucho, mQTL.NMR, facopy, cytofkit, GoogleGenomics, pbcmc, IrisSpatialFeatures

Thirteen software are deprecated in this release and will be removed in Bioc 3.10: flowQ, rMAT, TSSi, flowQB, rSFFreader, ProCoNA, spliceSites, GOTHiC, DOQTL, NGScopy, SVM2CRM, miRsponge, htSeqTools

Two experimental data packages were removed in this release (after being deprecated in BioC 3.8): iontreeData, MSBdata.

Two experimental data packages are deprecated in this release and will be removed in Bioc 3.10: PGPC, flowQBData

Two annotation packages were removed this release: MafDb.gnomADex.r2.0.1.hs37d5, MafDb.gnomAD.r2.0.1.hs37d5 (they were replaced with MafDb.gnomADex.r2.1.hs37d5, MafDb.gnomAD.r2.1.hs37d5)

Two annotation packages are deprecated in this release and will be removed in Bioc 3.10: MafDb.gnomADex.r2.0.1.GRCh38, MafDb.gnomAD.r2.0.1.GRCh38 (they have been replaced with MafDb.gnomADex.r2.1.GRCh38, MafDb.gnomAD.r2.1.GRCh38)