November 2, 2022

Bioconductors:

We are pleased to announce Bioconductor 3.16, consisting of 2183 software packages, 416 experiment data packages, 909 annotation packages, 28 workflows and 8 books.

There are 71 new software packages, 9 new data experiment packages, 1 new annotation packages, no new workflows, no new books, and many updates and improvements to existing packages.

Bioconductor 3.16 is compatible with R 4.2, and is supported on Linux, 64-bit Windows, and Intel 64-bit macOS 10.13 (High Sierra) or higher. Bioconductor is excited to start supporting arm64 with this release. This release will also include updated Bioconductor Docker containers.

Thank you to everyone for your contribution to Bioconductor

Visit Bioconductor BiocViews for details and downloads.

Contents

• Getting Started with Bioconductor 3.16
• New Software Packages
• New Data Experiment Packages
• New Annotation Packages
• New Workflow
• New Books
• NEWS from existing software packages
• NEWS from existing data experiment packages
• NEWS from existing workflows
• Deprecated and Defunct Packages

Getting Started with Bioconductor 3.16

To update to or install Bioconductor 3.16:

1. Install R 4.2. Bioconductor 3.16 has been designed expressly for this version of R.

2. Follow the instructions at Installing Bioconductor.

New Software Packages

There are 71 new software packages in this release of Bioconductor.

• ATACCoGAPS Provides tools for running the CoGAPS algorithm (Fertig et al, 2010) on single-cell ATAC sequencing data and analysis of the results. Can be used to perform analyses at the level of genes, motifs, TFs, or pathways. Additionally provides tools for transfer learning and data integration with single-cell RNA sequencing data.

• ATACseqTFEA Assay for Transpose-Accessible Chromatin using sequencing (ATAC-seq) is a technique to assess genome-wide chromatin accessibility by probing open chromatin with hyperactive mutant Tn5 Transposase that inserts sequencing adapters into open regions of the genome. ATACseqTFEA is an improvement of the current computational method that detects differential activity of transcription factors (TFs). ATACseqTFEA not only uses the difference of open region information, but also (or emphasizes) the difference of TFs footprints (cutting sites or insertion sites). ATACseqTFEA provides an easy, rigorous way to broadly assess TF activity changes between two conditions.

• BASiCStan Provides an interface to infer the parameters of BASiCS using the variational inference (ADVI), Markov chain Monte Carlo (NUTS), and maximum a posteriori (BFGS) inference engines in the Stan programming language. BASiCS is a Bayesian hierarchical model that uses an adaptive Metropolis within Gibbs sampling scheme. Alternative inference methods provided by Stan may be preferable in some situations, for example for particularly large data or posterior distributions with difficult geometries.

• BiocBaseUtils The package provides utility functions related to package development. These include functions that replace slots, and selectors for show methods. It aims to coalesce the various helper functions often re-used throughout the Bioconductor ecosystem.

• BiocFHIR FHIR R4 bundles in JSON format are derived from https://synthea.mitre.org/downloads. Transformation inspired by a kaggle notebook published by Dr Alexander Scarlat, https://www.kaggle.com/code/drscarlat/fhir-starter-parse-healthcare-bundles-into-tables. This is a very limited illustration of some basic parsing and reorganization processes. Additional tooling will be required to move beyond the Synthea data illustrations.

• BioNAR the R package BioNAR, developed to step by step analysis of PPI network. The aim is to quantify and rank each protein’s simultaneous impact into multiple complexes based on network topology and clustering. Package also enables estimating of co-occurrence of diseases across the network and specific clusters pointing towards shared/common mechanisms.

• cardelino Methods to infer clonal tree configuration for a population of cells using single-cell RNA-seq data (scRNA-seq), and possibly other data modalities. Methods are also provided to assign cells to inferred clones and explore differences in gene expression between clones. These methods can flexibly integrate information from imperfect clonal trees inferred based on bulk exome-seq data, and sparse variant alleles expressed in scRNA-seq data. A flexible beta-binomial error model that accounts for stochastic dropout events as well as systematic allelic imbalance is used.

• ccImpute Dropout events make the lowly expressed genes indistinguishable from true zero expression and different than the low expression present in cells of the same type. This issue makes any subsequent downstream analysis difficult. ccImpute is an imputation algorithm that uses cell similarity established by consensus clustering to impute the most probable dropout events in the scRNA-seq datasets. ccImpute demonstrated performance which exceeds the performance of existing imputation approaches while introducing the least amount of new noise as measured by clustering performance characteristics on datasets with known cell identities.

• CircSeqAlignTk CircSeqAlignTk is designed for end-to-end RNA-Seq data analysis of circular genome sequences, from alignment to visualization. It mainly targets viroids which are composed of 246-401 nt circular RNAs. In addition, CircSeqAlignTk implements a tidy interface to generate synthetic sequencing data that mimic real RNA-Seq data, allowing developers to evaluate the performance of alignment tools and workflows.

• consICA consICA implements a data-driven deconvolution method – consensus independent component analysis (ICA) to decompose heterogeneous omics data and extract features suitable for patient diagnostics and prognostics. The method separates biologically relevant transcriptional signals from technical effects and provides information about the cellular composition and biological processes. The implementation of parallel computing in the package ensures efficient analysis of modern multicore systems.

• crisprDesign Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences. This includes on- and off-target search, on-target efficiency scoring, off-target scoring, full gene and TSS contextual annotations, and SNP annotation (human only). It currently support five types of CRISPR modalities (modes of perturbations): CRISPR knockout, CRISPR activation, CRISPR inhibition, CRISPR base editing, and CRISPR knockdown. All types of CRISPR nucleases are supported, including DNA- and RNA-target nucleases such as Cas9, Cas12a, and Cas13d. All types of base editors are also supported. gRNA design can be performed on reference genomes, transcriptomes, and custom DNA and RNA sequences. Both unpaired and paired gRNA designs are enabled.

• crisprVerse The crisprVerse is a modular ecosystem of R packages developed for the design and manipulation of CRISPR guide RNAs (gRNAs). All packages share a common language and design principles. This package is designed to make it easy to install and load the crisprVerse packages in a single step. To learn more about the crisprVerse, visit https://www.github.com/crisprVerse.

• crisprViz Provides functionalities to visualize and contextualize CRISPR guide RNAs (gRNAs) on genomic tracks across nucleases and applications. Works in conjunction with the crisprBase and crisprDesign Bioconductor packages. Plots are produced using the Gviz framework.

• CTSV The R package CTSV implements the CTSV approach developed by Jinge Yu and Xiangyu Luo that detects cell-type-specific spatially variable genes accounting for excess zeros. CTSV directly models sparse raw count data through a zero-inflated negative binomial regression model, incorporates cell-type proportions, and performs hypothesis testing based on R package pscl. The package outputs p-values and q-values for genes in each cell type, and CTSV is scalable to datasets with tens of thousands of genes measured on hundreds of spots. CTSV can be installed in Windows, Linux, and Mac OS.

• demuxmix A package for demultiplexing single-cell sequencing experiments of pooled cells labeled with barcode oligonucleotides. The package implements methods to fit regression mixture models for a probabilistic classification of cells, including multiplet detection. Demultiplexing error rates can be estimated, and methods for quality control are provided.

• DNAfusion Paired-end sequencing of cfDNA generated BAM files can be used as input to discover EML4-ALK variants. This package was developed using position deduplicated BAM files generated with the AVENIO Oncology Analysis Software. These files are made using the AVENIO ctDNA surveillance kit and Illumina Nextseq 500 sequencing. This is a targeted hybridization NGS approach and includes ALK-specific but not EML4-specific probes.

• EasyCellType We developed EasyCellType which can automatically examine the input marker lists obtained from existing software such as Seurat over the cell markerdatabases. Two quantification approaches to annotate cell types are provided: Gene set enrichment analysis (GSEA) and a modified versio of Fisher’s exact test. The function presents annotation recommendations in graphical outcomes: bar plots for each cluster showing candidate cell types, as well as a dot plot summarizing the top 5 significant annotations for each cluster.

• eds This packages provides a single function, readEDS. This is a low-level utility for reading in Alevin EDS format into R. This function is not designed for end-users but instead the package is predominantly for simplifying package dependency graph for other Bioconductor packages.

• EpiMix EpiMix is a comprehensive tool for the integrative analysis of high-throughput DNA methylation data and gene expression data. EpiMix enables automated data downloading (from TCGA or GEO), preprocessing, methylation modeling, interactive visualization and functional annotation.To identify hypo- or hypermethylated CpG sites across physiological or pathological conditions, EpiMix uses a beta mixture modeling to identify the methylation states of each CpG probe and compares the methylation of the experimental group to the control group.The output from EpiMix is the functional DNA methylation that is predictive of gene expression. EpiMix incorporates specialized algorithms to identify functional DNA methylation at various genetic elements, including proximal cis-regulatory elements of protein-coding genes, distal enhancers, and genes encoding microRNAs and lncRNAs.

• epistasisGA This package runs the GADGETS method to identify epistatic effects in nuclear family studies. It also provides functions for permutation-based inference and graphical visualization of the results.

• factR factR contain tools to process and interact with custom-assembled transcriptomes (GTF). At its core, factR constructs CDS information on custom transcripts and subsequently predicts its functional output. In addition, factR has tools capable of plotting transcripts, correcting chromosome and gene information and shortlisting new transcripts.

• FuseSOM A correlation-based multiview self-organizing map for the characterization of cell types in highly multiplexed in situ imaging cytometry assays (FuseSOM) is a tool for unsupervised clustering. FuseSOM is robust and achieves high accuracy by combining a Self Organizing Map architecture and a Multiview integration of correlation based metrics. This allows FuseSOM to cluster highly multiplexed in situ imaging cytometry assays.

• gemma.R Low- and high-level wrappers for Gemma’s RESTful API. They enable access to curated expression and differential expression data from over 10,000 published studies. Gemma is a web site, database and a set of tools for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles.

• GenomAutomorphism This is a R package to compute the automorphisms between pairwise aligned DNA sequences represented as elements from a Genomic Abelian group. In a general scenario, from genomic regions till the whole genomes from a given population (from any species or close related species) can be algebraically represented as a direct sum of cyclic groups or more specifically Abelian p-groups. Basically, we propose the representation of multiple sequence alignments of length N bp as element of a finite Abelian group created by the direct sum of homocyclic Abelian group of prime-power order.

• ggtreeDendro Offers a set of ‘autoplot’ methods to visualize tree-like structures (e.g., hierarchical clustering and classification/regression trees) using ‘ggtree’. You can adjust graphical parameters using grammar of graphic syntax and integrate external data to the tree.

• goSorensen This package implements inferential methods to compare gene lists (in this first release, to prove equivalence) in terms of their biological meaning as expressed in the GO. The compared gene lists are characterized by cross-tabulation frequency tables of enriched GO items. Dissimilarity between gene lists is evaluated using the Sorensen-Dice index. The fundamental guiding principle is that two gene lists are taken as similar if they share a great proportion of common enriched GO items.

• HiCDOC HiCDOC normalizes intrachromosomal Hi-C matrices, uses unsupervised learning to predict A/B compartments from multiple replicates, and detects significant compartment changes between experiment conditions. It provides a collection of functions assembled into a pipeline to filter and normalize the data, predict the compartments and visualize the results. It accepts several type of data: tabular .tsv files, Cooler .cool or .mcool files, Juicer .hic files or HiC-Pro .matrix and .bed files.

• HiContacts HiContacts: R interface to (m)cool files and other Hi-C processed file formats. HiContacts provides a collection of tools to analyse and visualize Hi-C datasets. It can import data from pairs or (m)cool files.

• iSEEhex This package provides panels summarising data points in hexagonal bins for iSEE. It is part of iSEEu, the iSEE universe of panels that extend the iSEE package.

• iSEEhub This package defines a custom landing page for an iSEE app interfacing with the Bioconductor ExperimentHub. The landing page allows users to browse the ExperimentHub, select a data set, download and cache it, and import it directly into a Bioconductor iSEE app.

• ISLET ISLET is a method to conduct signal deconvolution for general -omics data. It can estimate the individual-specific and cell-type-specific reference panels, when there are multiple samples observed from each subject. It takes the input of the observed mixture data (feature by sample matrix), and the cell type mixture proportions (sample by cell type matrix), and the sample-to-subject information. It can solve for the reference panel on the individual-basis. It can also conduct test to identify cell-type-specific differential expression (csDE) genes.

• katdetectr Kataegis refers to the occurrence of regional hypermutation and is a phenomenon observed in a wide range of malignancies. Using changepoint detection katdetectr aims to identify putative kataegis foci from common data-formats housing genomic variants. Katdetectr has shown to be a robust package for the detection, characterization and visualization of kataegis.

• magrene magrene allows the identification and analysis of graph motifs in (duplicated) gene regulatory networks (GRNs), including lambda, V, PPI V, delta, and bifan motifs. GRNs can be tested for motif enrichment by comparing motif frequencies to a null distribution generated from degree-preserving simulated GRNs. Motif frequencies can be analyzed in the context of gene duplications to explore the impact of small-scale and whole-genome duplications on gene regulatory networks. Finally, users can calculate interaction similarity for gene pairs based on the Sorensen-Dice similarity index.

• metabinR Provide functions for performing abundance and compositional based binning on metagenomic samples, directly from FASTA or FASTQ files. Functions are implemented in Java and called via rJava. Parallel implementation that operates directly on input FASTA/FASTQ files for fast execution.

• MetaPhOR MetaPhOR was developed to enable users to assess metabolic dysregulation using transcriptomic-level data (RNA-sequencing and Microarray data) and produce publication-quality figures. A list of differentially expressed genes (DEGs), which includes fold change and p value, from DESeq2 or limma, can be used as input, with sample size for MetaPhOR, and will produce a data frame of scores for each KEGG pathway. These scores represent the magnitude and direction of transcriptional change within the pathway, along with estimated p-values.MetaPhOR then uses these scores to visualize metabolic profiles within and between samples through a variety of mechanisms, including: bubble plots, heatmaps, and pathway models.

• MsExperiment Infrastructure to store and manage all aspects related to a complete proteomics or metabolomics mass spectrometry (MS) experiment. The MsExperiment package provides light-weight and flexible containers for MS experiments building on the new MS infrastructure provided by the Spectra, QFeatures and related packages. Along with raw data representations, links to original data files and sample annotations, additional metadata or annotations can also be stored within the MsExperiment container. To guarantee maximum flexibility only minimal constraints are put on the type and content of the data within the containers.

• mslp An integrated pipeline to predict the potential synthetic lethality partners (SLPs) of tumour mutations, based on gene expression, mutation profiling and cell line genetic screens data. It has builtd-in support for data from cBioPortal. The primary SLPs correlating with muations in WT and compensating for the loss of function of mutations are predicted by random forest based methods (GENIE3) and Rank Products, respectively. Genetic screens are employed to identfy consensus SLPs leads to reduced cell viability when perturbed.

• MSstatsShiny MSstatsShiny is an R-Shiny graphical user interface (GUI) integrated with the R packages MSstats, MSstatsTMT, and MSstatsPTM. It provides a point and click end-to-end analysis pipeline applicable to a wide variety of experimental designs. These include data-dependedent acquisitions (DDA) which are label-free or tandem mass tag (TMT)-based, as well as DIA, SRM, and PRM acquisitions and those targeting post-translational modifications (PTMs). The application automatically saves users selections and builds an R script that recreates their analysis, supporting reproducible data analysis.

• NetActivity #’ NetActivity enables to compute gene set scores from previously trained sparsely-connected autoencoders. The package contains a function to prepare the data (prepareSummarizedExperiment) and a function to compute the gene set scores (computeGeneSetScores). The package NetActivityData contains different pre-trained models to be directly applied to the data. Alternatively, the users might use the package to compute gene set scores using custom models.

• octad OCTAD provides a platform for virtually screening compounds targeting precise cancer patient groups. The essential idea is to identify drugs that reverse the gene expression signature of disease by tamping down over-expressed genes and stimulating weakly expressed ones. The package offers deep-learning based reference tissue selection, disease gene expression signature creation, pathway enrichment analysis, drug reversal potency scoring, cancer cell line selection, drug enrichment analysis and in silico hit validation. It currently covers ~20,000 patient tissue samples covering 50 cancer types, and expression profiles for ~12,000 distinct compounds.

• omada Symptomatic heterogeneity in complex diseases reveals differences in molecular states that need to be investigated. However, selecting the numerous parameters of an exploratory clustering analysis in RNA profiling studies requires deep understanding of machine learning and extensive computational experimentation. Tools that assist with such decisions without prior field knowledge are nonexistent and further gene association analyses need to be performed independently. We have developed a suite of tools to automate these processes and make robust unsupervised clustering of transcriptomic data more accessible through automated machine learning based functions. The efficiency of each tool was tested with four datasets characterised by different expression signal strengths. Our toolkit’s decisions reflected the real number of stable partitions in datasets where the subgroups are discernible. Even in datasets with less clear biological distinctions, stable subgroups with different expression profiles and clinical associations were found.

• oncoscanR The software uses the copy number segments from a text file and identifies all chromosome arms that are globally altered and computes various genome-wide scores. The following HRD scores (characteristic of BRCA-mutated cancers) are included: LST, HR-LOH, nLST and gLOH. the package is tailored for the ThermoFisher Oncoscan assay analyzed with their Chromosome Alteration Suite (ChAS) but can be adapted to any input.

• PanViz This pacakge integrates data from the Kyoto Encyclopedia of Genes and Genomes (KEGG) with summary-level genome-wide association (GWAS) data, such as that provided by the GWAS Catalog or GWAS Central databases, or a user’s own study or dataset, in order to produce biological networks, termed IMONs (Integrated Multi-Omic Networks). IMONs can be used to analyse trait-specific polymorphic data within the context of biochemical and metabolic reaction networks, providing greater biological interpretability for GWAS data.

• phenomis The ‘phenomis’ package provides methods to perform post-processing (i.e. quality control and normalization) as well as univariate statistical analysis of single and multi-omics data sets. These methods include quality control metrics, signal drift and batch effect correction, intensity transformation, univariate hypothesis testing, but also clustering (as well as annotation of metabolomics data). The data are handled in the standard Bioconductor formats (i.e. SummarizedExperiment and MultiAssayExperiment for single and multi-omics datasets, respectively; the alternative ExpressionSet and MultiDataSet formats are also supported for convenience). As a result, all methods can be readily chained as workflows. The pipeline can be further enriched by multivariate analysis and feature selection, by using the ‘ropls’ and ‘biosigner’ packages, which support the same formats. Data can be conveniently imported from and exported to text files. Although the methods were initially targeted to metabolomics data, most of the methods can be applied to other types of omics data (e.g., transcriptomics, proteomics).

• proteasy Retrieval of experimentally derived protease- and cleavage data derived from the MEROPS database. Proteasy contains functions for mapping peptide termini to known sites where a protease cleaves. This package also makes it possible to quickly look up known substrates based on a list of (potential) proteases, or vice versa - look up proteases based on a list of substrates.

• RedisParam This package provides a Redis-based back-end for BiocParallel, enabling an alternative mechanism for distributed computation. The The ‘manager’ distributes tasks to a ‘worker’ pool through a central Redis server, rather than directly to workers as with other BiocParallel implementations. This means that the worker pool can change dynamically during job evaluation. All features of BiocParallel are supported, including reproducible random number streams, logging to the manager, and alternative ‘load balancing’ task distributions.

• regioneReloaded RegioneReloaded is a package that allows simultaneous analysis of associations between genomic region sets, enabling clustering of data and the creation of ready-to-publish graphs. It takes over and expands on all the features of its predecessor regioneR. It also incorporates a strategy to improve p-value calculations and normalize z-scores coming from multiple analysis to allow for their direct comparison. RegioneReloaded builds upon regioneR by adding new plotting functions for obtaining publication-ready graphs.

• RESOLVE Cancer is a genetic disease caused by somatic mutations in genes controlling key biological functions such as cellular growth and division. Such mutations may arise both through cell-intrinsic and exogenous processes, generating characteristic mutational patterns over the genome named mutational signatures. The study of mutational signatures have become a standard component of modern genomics studies, since it can reveal which (environmental and endogenous) mutagenic processes are active in a tumor, and may highlight markers for therapeutic response. Mutational signatures computational analysis presents many pitfalls. First, the task of determining the number of signatures is very complex and depends on heuristics. Second, several signatures have no clear etiology, casting doubt on them being computational artifacts rather than due to mutagenic processes. Last, approaches for signatures assignment are greatly influenced by the set of signatures used for the analysis. To overcome these limitations, we developed RESOLVE (Robust EStimation Of mutationaL signatures Via rEgularization), a framework that allows the efficient extraction and assignment of mutational signatures. RESOLVE implements a novel algorithm that enables (i) the efficient extraction, (ii) exposure estimation, and (iii) confidence assessment during the computational inference of mutational signatures.

• RgnTX RgnTX allows the integration of transcriptome annotations so as to model the complex alternative splicing patterns. It supports the testing of transcriptome elements without clear isoform association, which is often the real scenario due to technical limitations. It involves functions that do permutaion test for evaluating association between features and transcriptome regions.

• scBubbletree scBubbletree is a quantitative method for visual exploration of scRNA-seq data. It preserves biologically meaningful properties of scRNA-seq data, such as local and global cell distances, as well as the density distribution of cells across the sample. scBubbletree is scalable and avoids the overplotting problem, and is able to visualize diverse cell attributes derived from multiomic single-cell experiments. Importantly, Importantly, scBubbletree is easy to use and to integrate with popular approaches for scRNA-seq data analysis.

• scDDboost scDDboost is an R package to analyze changes in the distribution of single-cell expression data between two experimental conditions. Compared to other methods that assess differential expression, scDDboost benefits uniquely from information conveyed by the clustering of cells into cellular subtypes. Through a novel empirical Bayesian formulation it calculates gene-specific posterior probabilities that the marginal expression distribution is the same (or different) between the two conditions. The implementation in scDDboost treats gene-level expression data within each condition as a mixture of negative binomial distributions.

• scifer Have you ever index sorted cells in a 96 or 384-well plate and then sequenced using Sanger sequencing? If so, you probably had some struggles to either check the electropherogram of each cell sequenced manually, or when you tried to identify which cell was sorted where after sequencing the plate. Scifer was developed to solve this issue by performing basic quality control of Sanger sequences and merging flow cytometry data from probed single-cell sorted B cells with sequencing data. scifer can export summary tables, ‘fasta’ files, electropherograms for visual inspection, and generate reports.

• scMET High-throughput single-cell measurements of DNA methylomes can quantify methylation heterogeneity and uncover its role in gene regulation. However, technical limitations and sparse coverage can preclude this task. scMET is a hierarchical Bayesian model which overcomes sparsity, sharing information across cells and genomic features to robustly quantify genuine biological heterogeneity. scMET can identify highly variable features that drive epigenetic heterogeneity, and perform differential methylation and variability analyses. We illustrate how scMET facilitates the characterization of epigenetically distinct cell populations and how it enables the formulation of novel hypotheses on the epigenetic regulation of gene expression.

• ScreenR ScreenR is a package suitable to perform hit identification in loss of function High Throughput Biological Screenings performed using barcoded shRNA-based libraries. ScreenR combines the computing power of software such as edgeR with the simplicity of use of the Tidyverse metapackage. ScreenR executes a pipeline able to find candidate hits from barcode counts, and integrates a wide range of visualization modes for each step of the analysis.

• signifinder signifinder is an R package for computing and exploring a compendium of tumor signatures. It allows computing signatures scores providing the only gene expression values and returns a single-sample score. Currently, signifinder contains 46 distinct signatures collected from the literature.

• SimBu SimBu can be used to simulate bulk RNA-seq datasets with known cell type fractions. You can either use your own single-cell study for the simulation or the sfaira database. Different pre-defined simulation scenarios exist, as are options to run custom simulations. Additionally, expression values can be adapted by adding an mRNA bias, which produces more biologically relevant simulations.

• simpleSeg Image segmentation is the process of identifying the borders of individual objects (in this case cells) within an image. This allows for the features of cells such as marker expression and morphology to be extracted, stored and analysed. simpleSeg provides functionality for user friendly, watershed based segmentation on multiplexed cellular images in R based on the intensity of user specified protein marker channels. simpleSeg can also be used for the normalization of single cell data obtained from multiple images.

• spaSim A suite of functions for simulating spatial patterns of cells in tissue images. Output images are multitype point data in SingleCellExperiment format. Each point represents a cell, with its 2D locations and cell type. Potential cell patterns include background cells, tumour/immune cell clusters, immune rings, and blood/lymphatic vessels.

• SpatialFeatureExperiment A new S4 class integrating Simple Features with the R package sf to bring geospatial data analysis methods based on vector data to spatial transcriptomics. Also implements management of spatial neighborhood graphs and geometric operations. This pakage builds upon SpatialExperiment and SingleCellExperiment, hence methods for these parent classes can still be used.

• SPIAT SPIAT (Spatial Image Analysis of Tissues) is an R package with a suite of data processing, quality control, visualization and data analysis tools. SPIAT is compatible with data generated from single-cell spatial proteomics platforms (e.g. OPAL, CODEX, MIBI, cellprofiler). SPIAT reads spatial data in the form of X and Y coordinates of cells, marker intensities and cell phenotypes. SPIAT includes six analysis modules that allow visualization, calculation of cell colocalization, categorization of the immune microenvironment relative to tumor areas, analysis of cellular neighborhoods, and the quantification of spatial heterogeneity, providing a comprehensive toolkit for spatial data analysis.

• SpliceWiz Reads and fragments aligned to splice junctions can be used to quantify alternative splicing events (ASE). However, overlapping ASEs can confound their quantification. SpliceWiz quantifies ASEs, calculating percent-spliced-in (PSI) using junction reads, and intron retention using IRFinder-based quantitation. Novel filters identify ASEs that are relatively less confounded by overlapping events, whereby PSIs can be calculated with higher confidence. SpliceWiz is ultra-fast, using multi-threaded processing of BAM files. It can be run using a graphical user or command line interfaces. GUI-based interactive visualization of differential ASEs, including novel group-based RNA-seq coverage visualization, simplifies short-read RNA-seq analysis in R.

• SpotClean SpotClean is a computational method to adjust for spot swapping in spatial transcriptomics data. Recent spatial transcriptomics experiments utilize slides containing thousands of spots with spot-specific barcodes that bind mRNA. Ideally, unique molecular identifiers at a spot measure spot-specific expression, but this is often not the case due to bleed from nearby spots, an artifact we refer to as spot swapping. SpotClean is able to estimate the contamination rate in observed data and decontaminate the spot swapping effect, thus increase the sensitivity and precision of downstream analyses.

• Statial Statial is a suite of functions for identifying changes in cell state. The functionality provided by Statial provides robust quantification of cell type localisation which are invariant to changes in tissue structure. In addition to this Statial uncovers changes in marker expression associated with varying levels of localisation. These features can be used to explore how the structure and function of different cell types may be altered by the agents they are surrounded with.

• stJoincount stJoincount, the application of join count analysis to the spatial transcriptomics dataset. This tool converts the spatial map into a raster object (a two-dimensional image as a rectangular matrix or grid of square pixels), where clusters labelled spots are converted to adjacent pixels with a calculated resolution. A neighbors’ list was created based on the rasterized sample, which identifies adjacent and diagonal neighbors for each pixel. After adding binary spatial weights to the neighbors’ list, a multi-categorical join count analysis is then performed, allowing all possible combinations of cluster pairings to be tabulated. The function returns the observed join counts, the expected count under conditions of spatial randomness, and the variance of observed to expected calculated under non-free sampling. The z-score is then calculated as the difference between observed and expected counts, divided by the square root of the variance.

• SUITOR An unsupervised cross-validation method to select the optimal number of mutational signatures. A data set of mutational counts is split into training and validation data.Signatures are estimated in the training data and then used to predict the mutations in the validation data.

• syntenet syntenet can be used to infer synteny networks from whole-genome protein sequences and analyze them. Anchor pairs are detected with the MCScanX algorithm, which was ported to this package with the Rcpp framework for R and C++ integration. Anchor pairs from synteny analyses are treated as an undirected unweighted graph (i.e., a synteny network), and users can perform: i. network clustering; ii. phylogenomic profiling (by identifying which species contain which clusters) and; iii. microsynteny-based phylogeny reconstruction with maximum likelihood.

• TENxIO Provides a structured S4 approach to importing data files from the 10X pipelines. It mainly supports Single Cell Multiome ATAC + Gene Expression data among other data types. The main Bioconductor data representations used are SingleCellExperiment and RaggedExperiment.

• VDJdive This package provides functions for handling and analyzing immune receptor repertoire data, such as produced by the CellRanger V(D)J pipeline. This includes reading the data into R, merging it with paired single-cell data, quantifying clonotype abundances, calculating diversity metrics, and producing common plots. It implements the E-M Algorithm for clonotype assignment, along with other methods, which makes use of ambiguous cells for improved quantification.

• Voyager Voyager to SpatialFeatureExperiment (SFE) is just like scater to SingleCellExperiment. While SFE is a new S4 class, Voyager implements basic exploratory spatial data analysis (ESDA) methods for SFE. This first version supports univariate global spatial ESDA methods such as Moran’s I, permutation testing for Moran’s I, and correlograms. Voyager also implements plotting functions to plot SFE data and ESDA results. Multivariate ESDA and univariate local metrics will be added in later versions.

• vsclust Feature-based variance-sensitive clustering of omics data. Optimizes cluster assignment by taking into account individual feature variance. Includes several modules for statistical testing, clustering and enrichment analysis.

• zenith Zenith performs gene set analysis on the result of differential expression using linear (mixed) modeling with dream by considering the correlation between gene expression traits. This package implements the camera method from the limma package proposed by Wu and Smyth (2012). Zenith is a simple extension of camera to be compatible with linear mixed models implemented in variancePartition::dream().

New Data Experiment Packages

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

• BioPlex The BioPlex package implements access to the BioPlex protein-protein interaction networks and related resources from within R. Besides protein-protein interaction networks for HEK293 and HCT116 cells, this includes access to CORUM protein complex data, and transcriptome and proteome data for the two cell lines. Functionality focuses on importing the various data resources and storing them in dedicated Bioconductor data structures, as a foundation for integrative downstream analysis of the data.

• EpiMix.data Supporting data for the EpiMix R package. It include: - HM450_lncRNA_probes.rda - HM450_miRNA_probes.rda - EPIC_lncRNA_probes.rda - EPIC_miRNA_probes.rda - EpigenomeMap.rda - LUAD.sample.annotation - TCGA_BatchData - MET.data - mRNA.data - microRNA.data - lncRNA.data
  • Sample_EpiMixResults_lncRNA - Sample_EpiMixResults_miRNA - Sample_EpiMixResults_Regular - lncRNA expression data of tumors from TCGA that are stored in the ExperimentHub.

• HiContactsData Provides a collection of Hi-C files (pairs and (m)cool). These datasets can be read into R and further investigated and visualized with the HiContacts package. Data includes yeast Hi-C data generated by the Koszul lab from the Pasteur Institute.

• MerfishData MerfishData is an ExperimentHub package that serves publicly available datasets obtained with Multiplexed Error-Robust Fluorescence in situ Hybridization (MERFISH). MERFISH is a massively multiplexed single-molecule imaging technology capable of simultaneously measuring the copy number and spatial distribution of hundreds to tens of thousands of RNA species in individual cells. The scope of the package is to provide MERFISH data for benchmarking and analysis.

• MicrobiomeBenchmarkData The MicrobiomeBenchmarkData package provides functionality to access microbiome datasets suitable for benchmarking. These datasets have some biological truth, which allows to have expected results for comparison. The datasets come from various published sources and are provided as TreeSummarizedExperiment objects. Currently, only datasets suitable for benchmarking differential abundance methods are available.

• NetActivityData This package contains the weights from pre-trained shallow sparsely-connected autoencoders. This data is required for getting the gene set scores with NetActivity package.

• octad.db Open Cancer TherApeutic Discovery (OCTAD) package implies sRGES approach for the drug discovery. The essential idea is to identify drugs that reverse the gene expression signature of a disease by tamping down over-expressed genes and stimulating weakly expressed ones. The following package contains all required precomputed data for whole OCTAD pipeline computation.

• SFEData Example spatial transcriptomics datasets with Simple Feature annotations as SpatialFeatureExperiment objects. Technologies include Visium, slide-seq, Nanostring CoxMX, Vizgen MERFISH, and 10X Xenium. Tissues include mouse skeletal muscle, human melanoma metastasis, human lung, breast cancer, and mouse liver.

• WeberDivechaLCdata Spatially-resolved transcriptomics (SRT) and single-nucleus RNA-sequencing (snRNA-seq) data from the locus coeruleus (LC) in postmortem human brain samples. Data were generated with the 10x Genomics Visium SRT and 10x Genomics Chromium snRNA-seq platforms. Datasets are stored in SpatialExperiment and SingleCellExperiment formats.

New Annotation Packages

There are 2 new annotation packages in this release of Bioconductor.

• HDO.db A set of annotation maps describing the entire Human Disease Ontology assembled using data from DO. Its annotation data comes from https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/main/src/ontology.

• UniProtKeywords UniProt database provides a list of controlled vocabulary represented as keywords for genes or proteins. This is useful for summarizing gene functions in a compact way. This package provides data of keywords hierarchy and gene-keyword relations.

New Workflow Packages

There are no new workflow packages.

New Books

There are no new online books.

NEWS from existing Software Packages

affxparser

             Changes in version 1.69.1 (2022-04-28)                 

BUG FIXES

• Ported bug fix from affxparser 1.68.1.

             Changes in version 1.69.0 (2022-04-26)                 
  

• The version number was bumped for the Bioconductor devel version, which is now BioC 3.16 for R-devel.

             Changes in version 1.68.1 (2022-04-28)                 
  

BUG FIXES

• affxparser (>= 1.67.1) failed to install with R built with ‘-fpic’ flag. The symptom was a linking error ‘ld: 000.init.o: relocation R_X86_64_32 against `.rodata’ can not be used when making a shared object; recompile with -fPIC collect2: error: ld returned 1 exit status’.

alevinQC

                   Changes in version 1.13.2                        

• Allow processing of alevin-fry data with unfiltered permitlist

                   Changes in version 1.13.1                        
  

• Bug fix; use nbr mapped reads to calculate fraction of reads in barcode list for alevin-fry

AlpsNMR

             Changes in version 4.1.1 (2022-11-02)                  

• Remove archive dependency

• Try fixing build on palomino4, due to race condition in R CMD check

             Changes in version 3.99.7 (2022-10-27)                 
  

Minor changes

• Fix build issue on palomino4, simplifying helper function

             Changes in version 3.99.6 (2022-10-26)                 
  

Minor changes

• When saving, normalize extra information is saved as well.
• Updated downsampled demo data for examples.
• More robust nmr_baseline_threshold()

• Faster examples

             Changes in version 3.99.5 (2022-10-26)                 
  

Minor changes

• Remove call to deprecated ggplot2::qplot()

             Changes in version 3.99.4 (2022-10-19)                 
  

Major changes

• Improved the download_MTBLS242() function, allowing to either download the parts of MTBLS242 needed for the tutorial or the whole dataset, which may be nice to have if you want to play beyond the tutorial.

• When reading a Bruker sample from a zip file, you now can specify in the file name the zip subdirectory. For instance, “/path/to/sample.zip!/sample/3”, when sample.zip contains a folder named sample with a subfolder named 3 that includes the sample data you want to actually read.

Minor changes

• Remove Bioconductor Build System workaround, since https://github.com/Bioconductor/BBS/issues/220 was fixed.

             Changes in version 3.99.3 (2022-10-17)                 
  

• Add libarchive as a SystemRequirement to workaround a limitation of the Bioconductor build system (BBS), that can’t pick system requirements recursively. Thanks to Jennifer Wokaty for checking the BBS and providing this suggestion.

             Changes in version 3.99.2 (2022-10-14)                 
  

Breaking changes

• Set fix_baseline = FALSE in nmr_integrate_regions() as default. The former TRUE approach here did not make much sense if peak boundaries were not perfectly established.

Major changes

• Baseline estimation: We now offer nmr_baseline_estimation() besides nmr_baseline_removal(). The estimation function computes the baseline and saves it instead of subtracting it from the signal. This is a better approach because it lets each step of the pipeline decide whether it makes sense to subtract the baseline or not. The nmr_baseline_removal() is for now still available, but it will be deprecated in a future version.

• For the baselineThresh argument in nmr_detect_peaks() we now suggest using nmr_baseline_threshold(dataset, method = “median3mad”). This is more robust than the former (but still the default) method.

• Peak detection and integration: We want to approach the peak detection, clustering an integration in a different way. While the old pipeline still works as expected, we have introduced new arguments to peak detection, with backwards compatible defaults and a peak clustering function. We still provide the vignette with the former workflow, because it is still relevant but we may deprecate it in a future version, once we are confident the changes we are making are robust across several datasets.

• Parallellization: We are switching from the future package to BiocParallel, to better integrate in the Bioconductor ecosystem. In this version, if you use a different future plan you may get a warning to switch to BiocParallel. In a future version we will remove our dependency with the (awesome) future package.

Minor changes

• You can now set experiment names (NMRExperiment) with names(dataset) <- c(“Sample1”, “Sample2”).
• You can now pass a named vector with the sample names to the nmr_read_samples function. The names will be used as the sample names.
• Peak detection has a more robust baseline threshold estimation
• Peak detection estimates the baseline threshold on each sample individually. The threshold is calculated using only the sample where we are currently detecting the peaks.
• Peak detection includes a simple but effective lorentzian fitting (for area and width estimation)
• Add functions to evaluate the quality of the peak detection using plots
• More fine grained interpolation axis if axis = NULL is given in nmr_interpolate_1D()
• Save list of excluded regions in the nmr_dataset object.
• Drop MassSpecWavelet workaround on partial argument matching since it was fixed upstream
• Documentation: Start providing verbose messages with tips in functions
• Remove unused deprecated imports from the future package (#65, thanks to @HenrikBengtsson)
• Add URL and BugReports to the DESCRIPTION (#64, thanks to @HenrikBengtsson)
• Reading bruker samples is now a bit more robust and gives detailed tracebacks in case of error.

ANCOMBC

              Changes in version 2.0 (2022-10-19)                   

• add ancombc2 function

AnnotationForge

                   Changes in version 1.39.0                        

MODIFICATIONS

• 1.39.1 Update to REST query for uniprot

• 1.39.2 Update viableID.rda for upcoming release

AnnotationHub

                    Changes in version 3.5.0                        

NEW FEATURES

• (3.5.2) Add dcf dispatchclass

• (3.5.1) Add CompDb dispatchclass

AnVIL

                   Changes in version 1.10.0                        

NEW FEATURES

• (v 1.9.1) add drs_access_url() to returned signed https:// URLs from drs:// URIs. Enhance drs_cp().

• (v 1.9.4) add auto_unbox= argument to Service class, allowing other developers flexibility in unboxing values passed to REST APIs.

• (v 1.9.7) add developer facilities for tracking API changes in Rawls, Terra, and Leonardo services

USER VISIBLE CHANGES

• (v 1.9.2) Deprecate AnVIL::install() & friends in favor of BiocManager::install(), which now knows about container binary repositories.

• (v 1.9.8) Update Rawls, Terra, and Leonardo services. Changed endpoints include:

Rawls

$removed [1] admin_delete_refresh_token admin_statistics_get [3] refreshToken refreshTokenDate

$updated [1] listUserBillingAccounts createWorkspace getTags [4] clone entity_type_metadata get_entity [7] entityQuery createSubmission validateSubmission

Terra

$removed [1] userTrial listImportPFBJobs importPFBStatus

$updated [1] deleteBillingProject billingAccounts [3]] createWorkspace cloneWorkspace [5] entityQuery flexibleImportEntities [7] importEntities createSubmission [9] validateSubmission browserDownloadEntitiesTSV [11] setProfile

Leonardo

$removed [1] batchNodepoolCreate

$updated [1] listApp listAppByProject deleteApp [4] createApp listDisks listDisksByProject [7] createDisk updateRuntime createRuntime [10] setCookie proxyClusterJupyter proxyClusterJupyterLab [13] proxyClusterRStudio

• (v 1.9.9) add ‘gadgets’ (simple graphical interfaces) to key functions, avworkspace_gadget(), avtable_gadget(), avworkflow_gadget(). Also browse_workspace() for opening a terra workspace in the browser.

BUG FIXES

• (v 1.9.3 / 1.8.2) avworkflow_localize() looks for submissionId files correctly.

• (v 1.9.5 / 1.8.3) drs_stat() works when accessUrl is included in response.

• (v 1.9.6 / 1.8.5) gsutil_cp() and gsutil_rsync() use normalizePath() on source and destination arguments to avoid creating directories in unexpected locations when provided with paths containing ~, . or …

• (v 19.10 / v 1.8.6) gcloud_account(“<new account>”) did not invalidate cached access tokens. https://github.com/Bioconductor/AnVIL/issues/66

• (v 1.9.11 / v 1.8.7) avoid changing status of ‘Done’ workflows to ‘Aborted’ https://github.com/Bioconductor/AnVIL/issues/64

• (v 1.9.11 / v 1.8.7) allow ‘NULL’ for entity arguments of avworkflow_run() https://github.com/Bioconductor/AnVIL/issues/65

AnVILPublish

                    Changes in version 1.8.0                        

New Features

• (v. 1.7.1) Support publication output ‘.Rmd’

• (v. 1.7.2) Support ‘Quarto’ for Rmd to ipynb conversion

• (v. 1.7.3) Support ‘Qmd’ files.

User Visible Changes

• (v. 1.7.4) Update workspace publication – put ‘Description’ directly under title so it appears in WORKSPACE summary; add current ‘Date’ to citation if not already defined.

Bug Fixes

• (v. 1.7.4) Workspace dashboard and startup link to notebooks in ‘analysis’ rather than ‘notebook’ location; clean up vignette author list.

aroma.light

             Changes in version 3.27.0 (2022-04-26)                 

• The version number was bumped for the Bioconductor devel version, which is now BioC 3.16 for R-devel.

ATACCoGAPS

             Changes in version 0.99.0 (2022-03-04)                 

• Submitted to Bioconductor

ATACseqQC

                   Changes in version 1.21.2                        

• Add error message for NA seqlengths for factorFootprints.R

                   Changes in version 1.21.1                        
  

• remove the limits of BSgenome object for vPlot

AUCell

                    Changes in version 1.19                         

• New function: AUCell_assignCells()

bandle

                     Changes in version 1.1                         

bandle 1.1.3

• add more details in the documentation on how to fitGPs and pass hyppar to fitGPmaternPC
• updated typos in vignettes and removed calls to unecessary libraries
• added installation troubleshooting section to README to advise users of potential missing binary libraries

bandle 1.1.2

• fix bug in plotConvergence function

bandle 1.1.1

• use gh actions to build site

version 1.1.0

• fix typos
• upstream changes from bioconductor

BASiCS

             Changes in version 2.9.7 (2022-09-06)                  

• Bugfix in BASiCS_DetectHVG/BASiCS_DetectLVG.

             Changes in version 2.9.6 (2022-09-05)                  
  

• Add TransLogit parameter to BASiCS_PlotDE to have volcano plots on a logit scale. As the posterior probabilities are in the interval [0, 1] this may make it easier to visualise difference in “interesting” regions (e.g., 0.6-1)

             Changes in version 2.9.5 (2022-07-29)                  
  

• Further bugfix in subset method for BASiCS_Chain objects. subset now respects the ordering implied by character or numeric indices, where it previously did not.

             Changes in version 2.9.4 (2022-07-28)                  
  

• Update roxygen version

             Changes in version 2.9.3 (2022-07-18)                  
  

• Bugfix for divide and conquer code - handle arguments like StoreChains and RunName correctly in this context.

             Changes in version 2.9.2 (2022-07-18)                  
  

• Implement parallel tests

• Remove variance decomp plotting code from an internal code block to the public BASiCS_PlotVarianceDecomp.

             Changes in version 2.9.1 (2022-05-04)                  
  

• switch from using DOUBLE_EPS to a function call to std::numeric_limits<double>::epsilon() - credit Tomas Kalibera for informing by private correspondence.

BASiCStan

                     Changes in version 1.0                         

• Initial version with support for WithSpikes and Regression modes. No-spike version is supported with fixed scaling normalisation factors (scran size factors are used by default).

beachmat

                   Changes in version 2.14.0                        

• Added the tatami C++ library for LinkingTo from other packages.

BEclear

             Changes in version 2.13.2 (2022-09-21)                 

• fixed issue with tests

• fixed issue with folders

beer

             Changes in version 1.1.3 (2022-06-26)                  

• Added helper for plotting observed versus expected read counts (getExpected())

• Added helper for plotting Bayes factors (getBF())

             Changes in version 1.1.2 (2022-06-06)                  
  

• Added codetools to Suggests for BiocParallel dependency.

             Changes in version 1.1.1 (2022-06-06)                  
  

• Added support for running edgeR with glmQLFTest instead of exactTest.

benchdamic

             Changes in version 1.3.11 (2022-10-31)                 

• Updated DA_ANCOM with the new ancombc2 method

             Changes in version 1.3.10 (2022-10-20)                 
  

• Re-adapted p-values extraction from DA_ALDEx2() with test = “glm”

             Changes in version 1.3.9 (2022-09-18)                  
  

• Re-added corncob after temporary removal in v1.3.5

             Changes in version 1.3.8 (2022-09-18)                  
  

• Bug-fix for table headers in chapter 3 of the vignette

             Changes in version 1.3.7 (2022-09-18)                  
  

• Added more informations about the methods in chapter 3 of the vignette

             Changes in version 1.3.6 (2022-09-10)                  
  

• Simplified the vignette

             Changes in version 1.3.5 (2022-09-07)                  
  

• Temporarily removed corncob. New version of detectseparation v0.3 broke it.

• Updated intro vignette accordingly.

             Changes in version 1.3.4 (2022-09-07)                  
  

• Updated intro vignette.

• Removed HMP16SData chunks.

• Added conditional usage of kableExtra

• Removed dependency from HMP16SData and ffpe

• Implemented CAT function instead of using ffpe::CATplot

             Changes in version 1.3.3 (2022-09-06)                  
  

• In DA_basic changed logFC calculation when paired = TRUE

• In intro vignette corrected the number of comparisons from 10 to 2

             Changes in version 1.3.2 (2022-09-03)                  
  

• Changes after the first revision from the “Bioinformatics” journal

• Improved vignette with more descriptions, new methods, and more chapters

• Improved warning and error messages

• Support for TreeSummarizedExperiment object

• New function get_count_metadata() to access counts and metadata of a phyloseq or TreeSummarizedExperiment object.

• Added the “fitFeatureModel” implementation in DA_metagenomeSeq()

• “CSS” normalization factors are now returned as they are, not divided by a scaling factor

• Replaced “CSS_median” and “CSS_default” normalizations with “CSS”

• Added the “kw” and “glm” implementation in DA_ALDEx2()

• Added the “paired.test” option in DA_ALDEx2() for “t” and “wilcox” tests

• Added support for “CLR”, “RC”, and “none” normalization methods in DA_Seurat()

• Added support for “scale.factor” in DA_Seurat()

• Added more controls and verbosity regarding normalizations and DA methods

• Added the plotLogP() function for plottin the negative log p-values distribution

• Added DA_NOISeq(), DA_dearseq(), DA_ANCOM(), and DA_basic() to the pool of methods

• added detectseparation (<= 0.2.0) to the “Imports”, new version 0.3 not compatible with corncob 0.2

             Changes in version 1.3.1 (2022-05-16)                  
  

• Updated intro vignette

• Added more citations and authors

• Added figure captions and references

             Changes in version 1.3.0 (2022-04-26)                  
  

• Bump x.y.z version to odd y following creation of RELEASE_3_15 branch

             Changes in version 1.2.5 (2022-09-10)                  
  

• Porting the changes of devel version 1.3.6 to release

             Changes in version 1.2.4 (2022-09-07)                  
  

• Porting the changes of devel version 1.3.5 to release

             Changes in version 1.2.3 (2022-09-07)                  
  

• Porting the changes of devel version 1.3.4 to release

             Changes in version 1.2.2 (2022-09-06)                  
  

• Porting the changes of devel version 1.3.3 to release

             Changes in version 1.2.1 (2022-09-03)                  
  

• Porting the changes of devel version 1.3.2 to release

BindingSiteFinder

                     Changes in version 1.4                         

• major re-work of the vignette

• implemented bindingSiteCoveragePlot() function

• added subsetting by index functionalities

• parameters minCrosslinks and minClSites can be deactivated when set to 0

• coverageOverRanges() function fails with error message on subscript out of bounds

• fixed bug in ReproducibilityFilter() function

• fix silent option in BSFDataSet constructor

BiocBaseUtils

                    Changes in version 1.0.0                        

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

BiocCheck

                    Changes in version 1.34                         

NEW FEATURES

• Redundant package dependencies checks between DESCRIPTION and NAMESPACE have been removed. These are already present in R CMD check as “checking package dependencies”.

• Use callr to run BiocCheck in a separate process, this avoids interference with loaded packages (@vjcitn, #158)

BUG FIXES AND MINOR IMPROVEMENTS

• Update checkVigInstalls and checkVigBiocInst to avoid false positives (@almeidasilvaf, #170).

• Only count non evaluated chunks when there are any present in the vignette

• Fix false positive WARNING “Import {pkg} in NAMESPACE as well as DESCRIPTION.” where pkg was not in NAMESPACE but it was used using double colons pkg::function inside an S4 method. (@zeehio, #166)

• Fix bug where inputs to getDirFile were vectors in checkForValueSection (@zeehio, #163)

• Allow lookback for matching T/F and exclude list elements, e.g., list$F (@lshep, #161)

• Fix indentation count by excluding yaml front matter from vignettes (@harpomaxx, #100)

• Update internal documentation of the BiocCheck-class

• Fix bug where line numbers were off due to removal of empty lines at parsing (@lshep, #159)

• Slightly improve sentence counter for Description field check (@lshep, #160)

• Update documentation links to point to contributions.bioconductor.org (@LiNk-NY, #157)

BiocFHIR

                    Changes in version 1.0.0                        

• Specifically works with JSON data from https://synthea.mitre.org/downloads

BiocFileCache

                     Changes in version 2.5                         

ENHANCEMENT

• (2.5.2) Add option to override unique identifer when adding files to the cache. This will allow exact match of original file name.

BUG FIX

• (2.5.1) ERROR if interactively decide not to removebfc

BiocParallel

                    Changes in version 1.32                         

NEW FEATURES

• (v 1.31.10) bpiterate() when ITER is not a function will use bpiterateAlong() to attempt to iterate over elements ITER[[1]], ITER[[2]], etc. https://stat.ethz.ch/pipermail/bioc-devel/2022-July/019075.html

USER VISIBLE CHANGES

• (v 1.31.3) Deprecate BatchJobsParam in favor of BatchtoolsParam

• (v 1.31.11) Replace Random Number .Rnw vignette with Rmd (html) version (thanks Madelyn Carlson!) https://github.com/Bioconductor/BiocParallel/pull/215

• (v 1.31.12) clarify default number of cores, and use on shared clusters (thanks Dario Strbenac) https://github.com/Bioconductor/BiocParallel/pull/218 https://github.com/Bioconductor/BiocParallel/issues/217

• (v 1.31.15) Replace Introduction to BiocParallel .Rnw vignette with Rmd (html) version (thanks Phylis Atieno!) https://github.com/Bioconductor/BiocParallel/pull/226

BUG FIXES

• (v 1.31.1) suppress package startup messages on workers https://github.com/Bioconductor/BiocParallel/issues/198

• (v 1.31.1) coerce timeout to integer (typically from numeric) https://github.com/Bioconductor/BiocParallel/issues/200

• (v 1.31.2) avoid segfault when ipcmutex() functions generate C++ errors. This occurs very rarely, for instance when the directory used by boost for file locking (under /tmp) was created by another user. https://github.com/Bioconductor/BiocParallel/pull/202

• (v 1.31.2) resetting bpRNGseed() after bpstart() is reproducible https://github.com/Bioconductor/BiocParallel/pull/204

• (v 1.31.5) enable logs for multiple managers sharing the same workers. https://github.com/Bioconductor/BiocParallel/pull/207

• (v 1.31.13 / v 1.30.4) only export variables in .GlobalEnv or package: https://github.com/Bioconductor/BiocParallel/issues/223 https://github.com/Bioconductor/BiocParallel/pull/224

• (v 1.31.14) Reduce bpmapply memory usage. Thanks Sergio Oller. https://github.com/Bioconductor/BiocParallel/pull/227

BiocPkgTools

                   Changes in version 1.16.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• get_cre_orcids and orcid_table allow the querying of the ORCID API to obtain information about the maintainer whose ORCID is documented in the DESCRIPTION file (@vjcitn)

• biocBuildEmail now allows a to maintainer email override along with cc and bcc inputs.

• biocLastBuildDate gives the date of the last release build for a particular release version as shown in the bioconductor.org website

• The argument defaults for buildPkgDependencyDataFrame have changed to match that of tools::package_dependencies which is more appropriate for identifying “strong” dependencies (@vjcitn, #55).

• latestPkgStats, activitySince, and pkgDownloadRank are designed to pull package statistics from the GitHub API using gh packages or from Bioconductor. They are esp. useful for reporting to funding agencies.

biocthis

                    Changes in version 1.7.0                        

NEW FEATURES

• use_bioc_pkgdown_css(): helps you style your pkgdown website with Bioconductor colors. See https://github.com/lcolladotor/biocthis/issues/34 for details.
• use_bioc_badges(): helps you list all the Bioconductor badges (for software packages). See https://github.com/lcolladotor/biocthis/pull/35 for details.
• use_bioc_feature_request_template(): creates a feature request template for your GitHub repository. See https://github.com/lcolladotor/biocthis/pull/33 for details. use_bioc_issue_template() and use_bioc_support() were also updated to be more Bioconductor-centric.
• use_tinytest() adds support for tinytest. See https://github.com/lcolladotor/biocthis/pull/32 for details.

BUG FIXES

• Fixed pkgdown website creation. See https://github.com/lcolladotor/biocthis/issues/29 for details. This is also tangentially related to https://github.com/lcolladotor/biocthis/issues/31.
• Fixed usage of r-lib/actions. We now use v2. See https://github.com/lcolladotor/biocthis/issues/36, https://github.com/lcolladotor/biocthis/pull/37, and https://github.com/r-lib/actions/issues/639 for more.
• Thanks to everyone who contributed pull requests and GitHub issues!

biocViews

                   Changes in version 1.65.0                        

ENHANCEMENT

• (1.65.4) Change to allow Mac ARM64 binaries

• (1.65.2) Convert Sweave vignettes to Rmd

• (1.65.2) Add .gitignore

BioNAR

                  Changes in version 0.99.001                       

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

biosigner

                   Changes in version 1.25.6                        

MINOR MODIFICATION

• minor modification update

                   Changes in version 1.25.4                        
  

MINOR MODIFICATION

• biosigner.Rmd vignette: update

                   Changes in version 1.25.2                        
  

NEW FEATURE

• biosign: now handles SummarizedExperiment and MultiAssayExperiment instances

BridgeDbR

                    Changes in version 2.7.5                        

BUG FIXES

• Fixed a method definition

                    Changes in version 2.7.4                        
  

NEW FEATURES

• improved code

                    Changes in version 2.7.3                        
  

NEW FEATURES

• Updated to BridgeDb 3.0.14

• Support primary/secondary identifier annotation

• Added mapping Bioregistry.io compact identifiers

• Added getting a DataSource by their Bioregistry.io prefix

BUG FIXES

• Fixed some metadata in the package Rmd

cageminer

                    Changes in version 1.3.3                        

NEW FEATURES

• Added CITATION file linking to published paper.
• Increased unit test coverage to 100%.
• Changed pkgdown website template to match new standard of all of my packages.

Cardinal

             Changes in version 2.99.1 (2022-10-31)                 

SIGNIFICANT USER-VISIBLE CHANGES

• Updated vignettes for Cardinal 3

• Widened default m/z ‘tolerance’ for sparse spectra

• Switched to linear interpolation for sparse spectra

             Changes in version 2.99.0 (2022-10-26)                 
  

SIGNIFICANT USER-VISIBLE CHANGES

• Updated out-of-memory backend to Matter 2.0

• Removed support for legacy classes and methods

cbaf

             Changes in version 1.20.0 (2022-10-24)                 

New Features

• Introducing oneOfEach! using this option would force the availableData() to return one study for each cancer type that contain a technique of interest, instead of storing all the data in an excel file.

• It is now possible to generate Heatmap for a single gene.

cBioPortalData

                   Changes in version 2.10.0                        

New features

• Add cgdsr to cBioPortalData migration vignette (@kmezhoud, #54)
• Unmapped experiments are now added to the metadata in cBioDataPack
• Set default api. = api/v2/api-docs in cBioPortal to access the API protocol’s new location
• The fetchData developer function added to handle both molecularData and mutationData requests as deduced from the molecularProfileIds vector

Bug fixes and minor improvements

• Check for valid studyIds with getStudies in cBioDataPack
• ask argument correctly passed down to caching mechanism in cBioDataPack
• check_build option available in cBioDataPack particularly for new studies that have not been checked against.

celda

             Changes in version 1.13.0 (2022-10-20)                 

• Bug fixes related to cluster labels stored as factors and plotting
• Updated sparse matrix conversion to work with Matrix v1.4-2

CellBarcode

                    Changes in version 1.2.2                        

Enhancements

• Reduce memory usage by removing the original sequence in barcodeObj.

• Impromve fastq reading efficiency by using Rcpp.

New features

• bc_splitVDJ split VDJ barcode (experimental).

• bc_extract_10X_scSeq function used to extract transcripted barcode in 10X Genomics scRNASeq data.

Bug fix

• fix the error of bc_cure_cluster.

cellxgenedp

                     Changes in version 1.2                         

SIGNIFICANT USER-VISIBLE CHANGES

• (v. 1.1.4) allow custom files_download() cache. Thanks @stemangiola, https://github.com/mtmorgan/cellxgenedp/pull/9

• (v. 1.1.6) datasets ethnicity field renamed to self_reported_ethnicity

• (v. 1.1.7) use zellkonverter’s basilisk-based Python parser to read H5AD files in the vignette, see https://github.com/theislab/zellkonverter/issues/78

OTHER

• (v. 1.1.2) reset cache on build machines weekly

• (v. 1.1.6) use {rjsoncons} CRAN package for queries, rather than local implementation. Thanks @LiNk-NY, https://github.com/mtmorgan/cellxgenedp/pull/12

ChIPanalyser

                   Changes in version 1.19.0                        

Package Updates

• New model - integrating chromatin affinity and chromatin states

• Genetic algorithm to infer optimal paramters

ChIPpeakAnno

                   Changes in version 3.31.4                        

• update the oligoFrequency function to remove the limitation of sequence length

                   Changes in version 3.31.3                        
  

• support CSV format for toGRanges

                   Changes in version 3.31.2                        
  

• use ‘entrez_id’ instead of ‘EntrezID’ for getEnrichedPATH() output

                   Changes in version 3.31.1                        
  

• add parameter check of proximal.promoter.cutoff and immediate.downstream.cutoff for assignChromosomeRegion.

• fix the bug in plotBinOverRegions

ChIPQC

                   Changes in version 1.33.1                        

• Make use of BiocParallel more robust - now a Depends

• Bugfix for(is.na(peaks)) issue

ChIPseeker

                   Changes in version 1.33.4                        

• add citation Q. Wang (2022) (2022-10-29, Sat)

                   Changes in version 1.33.3                        
  

• allows passing user defined color to vennpie() (2022-10-20, Thu, #202, #207)
• add columns paramter to annotatePeak() to better support passing EnsDb to annoDb (#193, #205)

• export getAnnoStat() (#200, #204)

                   Changes in version 1.33.2                        
  

• supports by = “ggVennDiagram” in vennplot function (2022-09-13, Tue)

                   Changes in version 1.33.1                        
  

• plotPeakProf() allows passing GRanges object or a list of GRanges objects to TxDb parameter (2022-06-04, Sat)
• add test files for getTagMatrix() and plotTagMatrix()
• getBioRegion() supports UTR regions (3’UTR + 5’UTR)
• makeBioRegionFromGranges() supports generating windoes from self-made GRanges object
• allow specify colors in covplot() (2022-05-09, Mon, #185, #188)

CHRONOS

                   Changes in version 1.25.1                        

• Updated broken link in downloadKEGGPathwayList().

CircSeqAlignTk

             Changes in version 0.99.0 (2022-08-09)                 

• Released CircSeqAlignTk

ClassifyR

                    Changes in version 3.2.0                        

• Fast Cox survival analysis.

• Simple parameter sets, as used by crossVaildate, now come with tuning parameter grid as standard.

• Wrappers are greatly simplified. Now, there is only one method for a data frame and they are not exported because they are not used directly by the end-user anyway.

• prepareData function to filter and subset input data using common ways, such as missingness and variability.

• Invalid column names of data (e.g. spaces, hyphens) are converted into safe names before modelling but converted back into original names for tracking ranked and selected features.

• available function shows the keywords corresponding to transformation, selection, classifier functions.

• More functions have automatically-selected parameters based on input data, reducing required user-specified parameters.

• New classifiers added for random survival forests and extreme gradient boosting.

• Adaptive sampling for modelling with uncertainty of class labels can be enabled with adaptiveResamplingDelta.

• Parameter tuning fixed to only use samples from the training set.

cleaver

             Changes in version 1.35.1 (2022-08-31)                 

• Fix: adapt vignette code to new UniProt.ws.

clusterExperiment

                   Changes in version 2.17.3                        

• Fixed error in plotBarplot in handling non-assigned (-1) when comparing two clusterings (colors to clusters would be incorrect)

• Fixed error in subsetting of ClusterExperiment object if the unassigned cluster category (-1) was given a label in clusterLegend different than “-1” (would make those samples regular cluster).

clusterProfiler

                    Changes in version 4.5.3                        

• GSEA() supports GSONList object (2022-09-21, Wed)

• enricher() supports GSONList object (2022-09-06, Tue)

                    Changes in version 4.5.2                        
  

• support passing a GSON object to enricher(USER_DATA) and GSEA(USER_DATA) (2022-8-01, Mon)
• gson_kegg_mapper() allows building a gson object from outputs of KEGG Mapper service (2022-07-29, Fri, #492)
• fix show method for compareClusterResult (2022-06-21, Tue, #473)
• gson_KEGG() download latest KEGG and output a GSON object (2022-06-08, Wed)
• support passing a GSON object to gseKEGG(organism)

• support passing a GSON object to enrichKEGG(organism) (2022-06-06, Mon)

                    Changes in version 4.5.1                        
  

• follow KEGG api upgrade that change from http to https (2022-06-06, Mon)
• use ‘wininet’ to download KEGG data when .Platform$OS.type = “windows” (2022-06-03, Fri)
• mv read.gmt and read.gmt.wp to the ‘gson’ package and reexport these two functions from ‘gson’ (2022-04-28, Thu)
• fix compareCluster when fun = enrichPathway(2022-4-28, Thu)

CNVfilteR

                   Changes in version 1.11.1                        

BUG FIXES

• Minor bug fixed: now loadVCFs() properly overwrites vcf and generates tabix files if temp dir is used. It prevents an unlikely but unwanted situation: when, in a same R session, a user updates VCF content without renaming it. In this case, file already existed and the new VCF/GZ file was not being used by CNVfilteR.

cogeqc

                    Changes in version 1.1.8                        

CHANGES

• Synteny assessment formula now also considers scale-free topology fit.

BUG FIXES

• Reference-based orthogroup inference does not require the exact same set of species anymore.

                    Changes in version 1.1.7                        
  

BUG FIXES

• Variable Duplications_50 of the duplications data frame was not matching variable Dups of the stats data frame in the output of read_orthofinder_stats()

NEW FEATURES

• Replaced dispersal formula with a more meaningful and interpretable one.

• Added a max_size param to plot_og_sizes() to ignore OGs larger than a specific size.

                    Changes in version 1.1.4                        
  

NEW FEATURES

• Added option to scale scores by the maximum value

                    Changes in version 1.1.3                        
  

NEW FEATURES

• Added a correction for overclustering in calculate_H() that penalizes protein domains in multiple orthogroups.
• Updated vignette to provide a detailed explanation of how homogeneity scores are calculated.

coMET

             Changes in version 1.29.2 (2022-10-26)                 

• Remove dependancy colortools

• Add functions to replace the package colortools

compEpiTools

                   Changes in version 1.31.1                        

• The following function is updated
  • GRbaseCoverage/GRcoverage/GRenrichment: The maxDepth setting of ApplyPileupsParam was raised to 1000000

ComplexHeatmap

                   Changes in version 2.13.4                        

• anno_barplot(): fixed a bug when split is set, the bars are wrongly plotted under besides = TRUE.

• anno_boxplot(): add two new argumetn: add_points and pt_gp.

• fixed a bug of size of column title wrongly calculated.

                   Changes in version 2.13.2                        
  

• HeatmapAnnotation(): fixed a bug where annotation legends are not all generated when df is set.

• UpSet(): now bg_col can be a vector of length more than two.

• oncoPrint(): Add pct_include argument.

• anno_density(): fixed a bug where xlim is ignored for “heatmap”.

                   Changes in version 2.13.1                        
  

• column_title_rot can be set with any degree value.

• automatically recognize Jupyter environment.

• UpSet(): comb_col now is correctly assigned when the combination matrix is transposed.

CompoundDb

                     Changes in version 1.1                         

Changes in version 1.1.6

• CompDb tests also for NA input.

Changes in version 1.1.5

• MsBackendCompDb always returns collisionEnergy as numeric.

Changes in version 1.1.4

• Add script to create a CompDb from a MassBank database.

Changes in version 1.1.3

• Expand vignette with examples to create CompDb databases from scratch.

Changes in version 1.1.2

• Add insertCompound and deleteCompound functions to add or remove compounds from a CompDb or IonDb.

Changes in version 1.1.1

• Fix wrong warning message in deleteIon.
• Change database data type for internal ion_id from character to integer.

CoreGx

                    Changes in version 2.1.7                        

• Fixed a bug when deleting a TreatmentResponseExperiment assay via NULL assignment
• Added a names S4 method fo TreatmentResponseExperiment to enable tab autocomplete with $ access in interative sessions
• Added additional methods for drug combination modelling; these changes will be documented in a new vignette once we have thoroughly tested the new functions

• For now these are experimental and should not be considered a stable API

                    Changes in version 2.1.6                        
  

• Changed default parallelization strategy inside aggregate2 (and therefore inside aggregate,TreatmentResponseExperiment-method and endoaggregate) to split the table into nthread tables instead of using by
• Result should be (1) parallelization is now always faster than serial computations, which was not true previously
• Memory usage of parallelization should be much smaller, since we aren’t splitting into a very long list of tables
• Optimized the internal representation of the TreatmentResponseExperiment assay index to remove storage of NA for rowKey-colKey combinations with no observations in any assay
• This was causing memory usage to baloon if both rowKey and colKey were a large sequence
• Prepended a “.” to the internal assay index column names for each assay

• This should reduce name clashes between internal TRE metadata and the column names of an assay (specifically, you can now have a column with the same name as the assay)

                    Changes in version 2.1.5                        
  

• Add error message to CoreSet,show-method which lets users know to use updateObject if the slot names are not valid

                    Changes in version 2.1.4                        
  

• Add endoaggregate method to compute TreatmentResponseExperiment assay aggregations within the object

• Add mergeAssays method to allow joining assaying within a TreatmentResponseExperiment

                    Changes in version 2.1.3                        
  

• Updated CoreSet vignette to reflect recent changes to the object structure
• Renamed the LongTable vignette to TreatmentResponseExperiment and updated the content to reflect the changes in class structure from 2.1.1
• Generated new TreatmentResponseExperiment class and structure diagrams and inlcuded them in the TreamentResponseExperiment vignette
• Added new example TreatmentResponseExperiment object to package data
• Added various unit tests for the LongTable (and therefore also the TreatmentResponseExperiment)
• Added proper documentation object for the TREDataMapper-accessors
• Added aggregate methods for data.table and LongTable
• Added endoaggregate method for LongTable, which uses aggregate internally but assigns the result back to the object and returns the updated object. Thus this method is an endomorphic version of aggregate.
• Added new argument summarize to assay,LongTable-method which only attaches columns which have been summarized over if FALSE

• Added assayCols and assayKeys helper methods to retrive valid assay column names or the key columns for an assay, respectively.

                    Changes in version 2.1.2                        
  

• Fix bug in logLogisticRegression causing tests to fail in Bioconductor 3.16 daily builds

                    Changes in version 2.1.1                        
  

• First update since Bioconductor 3.15 release
• Merged rework of the LongTable class back into main branch
• The object has now been updated to

cTRAP

                   Changes in version 1.14.1                        

• Add cTRAP version to welcome modal
• Fix crash when submitting Celery job (included missing floweRy function)
• Fix large JSON responses from DT blocked by reverse proxy default settings

cytomapper

             Changes in version 1.9.2 (2022-10-24)                  

• measureObjects accounts for single objects in images

             Changes in version 1.9.1 (2022-07-24)                  
  

• measureObjects function transfers mcols of images and masks to colData(sce)

• allow returned object to be of SpatialExperiment

CytoML

                    Changes in version 3.11                         

API Changes

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

Fixes/internal changes

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

• Add CytoML XSD to installation

                    Changes in version 3.10                         
  

API Changes

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

• Renaming of methods:

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

• compare.counts -> gs_compare_cytobank_counts

• Renaming of classes:

• divaWorkspace -> diva_workspace

• flowJoWorkspace -> flowjo_workspace

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

Fixes/internal changes

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

dagLogo

                   Changes in version 1.35.1                        

• Update uniprot rest api.

dcanr

             Changes in version 1.14.0 (2022-10-11)                 

• Removed implementation for the ECF method as the package for computing the statistic, COSINE, is now deprecated
• Added a method to run the z-score method with greater flexibility

dearseq

             Changes in version 1.9.4 (2022-07-20)                  

• use scattermore in plot_weights()

             Changes in version 1.8.3 (2022-07-13)                  
  

• fixed a bug in NA handling with which_weights != “none”

             Changes in version 1.8.1 (2022-04-28)                  
  

• fixed a small bug in permutation p-values introduced with the 1.8.0 release

decompTumor2Sig

             Changes in version 2.13.1 (2022-05-09)                 

• Fix: corrected recognition of EstimatedParameters (from package pmsignature) objects obtained with the use of a background signature.

• Fix: corrected internal scripts for production of external example data.

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”)

             Changes in version 1.42.1 (2022-05-31)                 
  

Bugfixes

• Fully adjust VCF creation to use VariantAnnotation 1.27.6 and later’s API (fixes broken VCF output like ##fileformat=<ID=fileformat,Value=VCFv4.1>)

• Fix crash when encountering reads that don’t have an NM field

• Fix crash when compiled with CentOS 8’s GCC 8.3.1-4

• Correct the template VCF files’ #CHROM header lines

DegNorm

                    Changes in version 1.7.1                        

• .gtf_parse function has been updated so overlapping exons are merged in total transcript

DEGreport

                   Changes in version 1.33.2                        

• Remove lasso2 from dependencies

                   Changes in version 1.33.1                        
  

• Remove Nozzle.R1 from dependencies

DelayedArray

                   Changes in version 0.24.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Move the aperm() S4 generic to BiocGenerics.

DExMA

                    Changes in version 1.5.1                        

• Improvement of some functions

• Remove seeCov function

• ACAT p-values combination method added

• Imputation indicators added to the missGenesImput fucntion

DiffBind

                     Changes in version 3.8                         

• Rollover bugfixes from Release branch

• Re-normalize after applying black/greylists

• Apply Rhtslib patch

• Update vignette

• Remove contact info for Gord

DifferentialRegulation

                    Changes in version 1.0.7                        

• bug (prompting when analyzing 1 cluster only) in DifferentialRegulation function fixed

                    Changes in version 1.0.6                        
  

• bug giving error (in plot_pi function) fixed

                    Changes in version 1.0.5                        
  

• information about convergence added (in DifferentialRegulation function)

                    Changes in version 1.0.4                        
  

• bug giving error (in DifferentialRegulation function) fixed

                    Changes in version 1.0.3                        
  

• vignettes extended

                    Changes in version 1.0.2                        
  

• function ‘plot_pi’ added

                    Changes in version 1.0.1                        
  

• memory usage (of DifferentialRegulation function) reduced

Dino

                    Changes in version 1.3.1                        

• Bug fix for input data formats: matrices with named rownames and DelayedMatrix
• Vignette updates
• Citation updates
• Contact updates

dittoSeq

                    Changes in version 1.10                         

• Added ability to plot multiple ‘var’ in a single ‘dittoPlot()’, ‘dittoDimPlot()’, ‘dittoScatterPlot()’, ‘dittoDimHex()’, and ‘dittoScatterHex()’ call by giving a vector of genes or continuous metadata to the ‘var’ or ‘color.var’ input. Customization of how the “multivar” data is displayed can be controlled with: 1- ‘multivar.aes’ (context: ‘dittoPlot()’ only) - which plot aesthetic is utilized for displaying var-values. 2- ‘multivar.split.dir’ - faceting direction to use for var-data when combining with an additional ‘split.by’ variable.
• Improved the compatibility with ‘split.by’/faceting customizations, specifically with ‘split.adjust = list(scales = “free”)’, by making implementations of ‘min’/’max’ inputs less intrusive. Note: This change very minorly alters the default output of some plotters.
• Improved error messaging for cases where ‘object’ does not have cell/column names.

DOSE

                   Changes in version 3.23.3                        

• replace DO.db to HDO.db (2022-10-7, Fri)
• add values of organism, keytype and setType for GSEA_internal() (2022-09-21, Wed)
• add values of organism, keytype and ontology for enricher_internal() (2022-09-21, Wed)
• move inst/extdata/parse-obo.R to HDO.db package (2022-08-29, Mon)

• rename qvalues to qvalue in gseaResult object (2022-08-29, Mon)

                   Changes in version 3.23.2                        
  

• Support GSON object in GSEA_internal() (2022-06-08, Wed)

                   Changes in version 3.23.1                        
  

• Support GSON object in enricher_internal() (2022-06-06, Mon)

DropletUtils

                   Changes in version 1.18.0                        

• Added an intersect.genes= option to read10xCounts() for samples with inconsistent gene information. Automatically fix empty chromosome names for mitochondrial genes in certain Cellranger outputs.

edgeR

                   Changes in version 3.40.0                        

• New argument ‘hairpinBeforeBarcode’ for processAmplicons(). The revised function can process reads where the hairpins/sgRNAs/sample index sequences are in variable positions within each read. When ‘plotPositions=TRUE’ a density plot of the match positions is created to allow the user to assess whether they occur in the expected positions.

• Update C++ BLAS calls to account for USE_FC_LEN_T setting in R 4.3.0.

• Bug fix to R_compute_apl.cpp to make sure GLM working weights are zero when fitted mu=0.

enrichplot

                   Changes in version 1.17.4                        

• rename parameters of emapplot(), centplot() and treeplot() (2022-09-11, Sun)

                   Changes in version 1.17.3                        
  

• align the dots in treeplot() (2022-10-1, Sat)

• fix a bug in color legend of treeplot() (2022-10-1, Sat)

                   Changes in version 1.17.2                        
  

• autofacet to automatically split barplot and dotplot into several facets (2022-09-06, Tue)
• dotplot method for enrichResultList object
• add parameters hilight_category, alpha_hilight, alpha_nohilight for cnetplot() and emapplot (2022-09-4, Sun)
• change round digits of cnetplot scatterpie legend to 1 (2022_8_29, Mon).
• gsearank() can export result as a table when output = “table” (2022-08-29, Mon, #184)
• fix a bug in fc_readable() (2022-08-29, Mon, #189)

• allows passing color=”NES” to dotplot() for gseaResult object (2022-08-29, Mon, #14)

                   Changes in version 1.17.1                        
  

• fix a bug in https://github.com/YuLab-SMU/clusterProfiler/issues/488 (2022-08-25, Thu)
• support multiple gene sets in geom_gsea_gene layer (2022-08-25, Thu)
• geom_gsea_gene layer (2022-08-24, Wed)
• add parameters symbol and pvalue for heatplot.enrichResult() (2022-08-20, Sat)
• change default values of group_category and node_label in ssplot() (2022-07-04, Mon)
• update document of ssplot() (2022-07-04, Mon)
• gseaplot() and gseaplot2() return gglist object instead of plotting the figure (2022-05-05, Thu)
• fix ridgeplot when x@readable = TRUE (2022-04-30, Sat)

ensembldb

                   Changes in version 2.21.5                        

• Fix spell mistakes (thanks to Mike Love).

                   Changes in version 2.21.3                        
  

• Add minimal required Ensembl API version for certain data fields (stable_id_version). Issue https://github.com/jorainer/ensembldb/issues/139

                   Changes in version 2.21.1                        
  

• Since is circular flag for chromosomes extracted using the Ensembl Perl API is always FALSE: manually set isCircular to TRUE for chromosome(s) named "MT" (issue https://github.com/jorainer/ensembldb/issues/133).

EpiCompare

                    Changes in version 1.1.2                        

New features

• rebin_peaks:
• Added arg drop_empty_chr to automatically drop chroms that aren’t in any of the peakfiles.
• Added “score” as one of the default intensity_cols in all relevant functions.
• Make examples use 5000bp bins to speed up.
• translate_genome:
• Add default_genome arg to handle genome=NULL.
• bpplapply:
• New exported function to automate handling of known issues with BiocParallel across OS platforms.
• Enable users to specify their own apply function.
• get_bpparam: Add args to allow users to choose which BiocParallel func to use.
• checkCache: Make default arg cache=BiocFileCache::BiocFileCache(ask = FALSE) to skip user input during runtime.
• precision_recall:
• Change increment_threshold arg to n_threshold arg, using the seq(length.out=) feature to avoid accidentally choosing an inappropriately large increment_threshold.
• gather_files:
• Replace iterator with bpplapply.
• Pass up args from bpplapply.
• Provide warning message, not error, when 0 files found. Returns NULL.
• Add “multiqc” as a search option.
• Add dedicated subfunctions for reading in a variety of nf-core/cutandrun outputs files: read_picard,read_multiqc,read_bowtie, read_trimgalore,read_bam,read_peaks
• Add file paths to each object.
• Add new arg rbind_list.
• rebin_peaks/compute_corr: -Change defaultbin_size from 100 –> 5kb to improve efficiency and align with other defaults of other packages (e.g Signac).
• tss_plot:
• Pass up more arg for specifying upstream/downstream.
• EpiCompare: Pass up new args:
• bin_size
• n_threshold
• workers

Bug fixes

• Fix rebin_peaks unit tests.
• Fix pkg size issue by adding inst/report to .Rbuildignore.
• EpiCompare wasn’t being run when reference was a single unlisted GRanges object because it was indeed length>1, but the names were all NULL. Now fixed.
• plot_precision_recall: Set default initial_threshold= to 0.

• Switch from BiocParallel to parallel, as the former is extremely buggy and inconsistent.

                    Changes in version 1.1.1                        
  

New features

• check_genome_build: Add translate_genome as prestep.
• rebin_peaks:
  1. Move all steps that could be done just once (e.g. creating the genome-wide tiles object) outside of the BiocParallel::bpmapply iterator.
  2. Ensure all outputs of BiocParallel::bpmapply are of the same length, within the exact same bins, so that we can return just the bare minimum data needed to create the matrix (1 numeric vector/sample).
  3. Instead of rbinding the results and then casting them back into a matrix (which is safer bc it can handle vectors of different lengths), simply cbind all vectors into one matrix directly and name the rows using the predefined genome-wide tiles.
  4. Because we are no longer rbinding a series of very long tables, this avoids the issue encountered here #103. This means this function is now much more scalable to many hundreds/thousands of samples (cells) even at very small bin sizes (e.g. 100bp).
  5. A new argument keep_chr allows users to specify whether they want to restrict which chromosomes are used during binning. By default, all chromosomes in the reference genome are used (keep_chr=NULL), but specifying a subset of chromosomes (e.g. paste0(“chr”,seq_len(12))) can drastically speed up compute time and reduce memory usage. It can also be useful for removing non-standard chromosomes (e.g. “chr21_gl383579_alt”, “chrUns…”, “chrRand…”).
  6. As a bonus, rebin_peaks now reports the final binned matrix dimensions and a sparsity metric.
• compute_corr:
• Added unit tests at different bin sizes.
• Allow reference to be NULL.
• Updated README to reflect latest vesion of EpiCompare with gather_files.

Bug fixes

• Bumped version to align with Bioc devel (currently 1.1.0).
• compute_percentiles:
• Making default initial_threshold=0, so as not to assume any particular threshold.
• rebin_peaks:
• Addressed error that occurs when there’s many samples/cells with small bins.
• plot_precision_recall: Don’t plot the reference as part of the PR curve.

epimutacions

                    Changes in version 1.1.2                        

• Get plots fixed
• Get annotation fixed
• Removed extra slashes from annotations

EWCE

                    Changes in version 1.5.8                        

Bug fixes

• GHA fix.

                    Changes in version 1.5.7                        
  

Bug fixes

• orthogene dependency has been replacing user entered background gene list with one generated from all known genes when species across gene lists and reference dataset are the same. This has now been fixed.

                    Changes in version 1.5.5                        
  

Bug fixes

• standardise_ctd:

• Always force “specificity_quantiles” to be one of the matrices in each level.

                    Changes in version 1.5.4                        
  

New features

• filter_ctd_genes
• Now exported.
• Can handle standardized CTD format.
• get_ctd_matrix_names: New function to get a list of all data matrices in CTD.

Bug fixes

• check_ewce_genelist_inputs:
• User reported potential bug in code:https://github.com/NathanSkene/EWCE/issues/71
• Fixed by removing conditional and instead always filtering out genes not present in CTD/SCT.
• standardise_ctd:
• Add check_species()
• Ensure all matrices become sparse when as_sparse=TRUE.
• Generalize to matrices of any name.
• fix_celltype_names:

• Ensure all celltype names are unique after standardization.

                    Changes in version 1.5.3                        
  

New features

• genelistSpecies now passed to prepare_genesize_control_network in bootstrap_enrichment_test meaning gene list species will be inferred from user input.

                    Changes in version 1.5.2                        
  

New features

• drop_uninformative_genes:
• Expose new args: dge_method, dge_test, min_variance_decile
• merged_ctd: Actually merge the CTDs into one when as_SCE=FALSE.

Bug fixes

• Remove hard-coded file path separators (e.g. sprintf(“%s/MRK_List2.rpt”, tempdir())) to be more compatible with Windows.

                    Changes in version 1.5.1                        
  

New features

• Made substantial updates to orthogene, so going through and making sure everything still works / is able to take advantage of new features (e.g. separation of non121_strategy and agg_func args, many:many mapping):
• filter_nonorthologs: Pass up args from orthogene::convert_orthologs.
• generate_celltype_data: @inheritDotParams
• Update GHA.
• Bump to R (>= 4.2) now that we’re developing on Bioc 3.16.

Bug fixes

• Avoid downloading large “MRK_List2.rpt” file any more than is necessary for testing.

exomePeak2

             Changes in version 1.8.1 (2022-05-16)                  

• Add parameters to initiate mode of motif based analysis.

• Add parameters to configure saving directories.

• Fix saving issue when -log pvalues have NA/NaN (no change in default method).

ExploreModelMatrix

                    Changes in version 1.9.2                        

• Fix inconsistency in cooccurrence plots obtained when providing the design matrix directly, if the sample table contained additional columns not used for the design matrix.

extraChIPs

             Changes in version 1.1.5 (2022-10-11)                  

• Added makeConsensus() and updated vignette

             Changes in version 1.1.3 (2022-08-01)                  
  

• Added plotOverlaps() for generation of Venn Diagrams and ComplexUpset plots

             Changes in version 1.1.2 (2022-07-22)                  
  

• Added collapseTranscripts = “auto” as the default for plotHFGC()
• getProfileData() now returns log2 transformed data by default
• getProfileData() now uses bplapply() internally

• Bugfixes for plotPie(), distinctMC() colToRanges() and stitchRanges()

             Changes in version 1.1.1 (2022-06-01)                  
  

• Bugfix so as_tibble() respects original column names

fastreeR

             Changes in version 1.3.0 (2022-11-01)                  

• Bump x.y.z version to odd y following creation of RELEASE_3_16 branch.

             Changes in version 1.2.0 (2022-11-01)                  
  

• Bump x.y.z version to even y prior to creation of RELEASE_3_16 branch.

             Changes in version 1.1.6 (2022-09-26)                  
  

• Update java backend to BioInfoJavaUtils-1.2.4 (revamped FastaManager).

             Changes in version 1.1.5 (2022-06-23)                  
  

• Update vignette minor bug.

             Changes in version 1.1.4 (2022-06-16)                  
  

• Update vignette to handle getting sample files through https failure.

             Changes in version 1.1.3 (2022-06-06)                  
  

• Update vignette to handle getting sample files through https failure.

             Changes in version 1.1.2 (2022-05-15)                  
  

• Update possibly corrupted samples.vcf.gz.

             Changes in version 1.1.1 (2022-05-08)                  
  

• Update tests to improve coverage.

             Changes in version 1.1.0 (2022-05-08)                  
  

• Bump x.y.z version to odd y following creation of RELEASE_3_15 branch.

fgga

             Changes in version 1.5.0 (2022-07-13)                  

• Made the following significant changes o changed the names of the varianceSVM and svmSVM functions to varianceOnto and svmOnto respectively o added the PO, ZFA and HPO ontologies to the preCoreFG function o added functions to evaluate the performance of the classification process

fgsea

                   Changes in version 1.23.1                        

• Introduced GESECA method for multi-conditional gene set enrichment (see geseca-tutorial vignette for details)

• Enrichment table plots now use cowplot (issue #101)

• Enrichment table plots are more easily fine-tuned (issue #29)

FindIT2

                    Changes in version 1.2.3                        

• fix a bug when Txdb have no gene scaffold

                    Changes in version 1.2.1                        
  

• add FindIT2 publication info so people can cite

fishpond

                    Changes in version 2.4.0                        

• For simple paired swish analysis, adding a fast=1 method which uses a one-sample z-score on the paired LFCs (averaged over samples, then median over inferential replicates). The permutation is computed by changing the signs of the LFC matrix and recomputing z-scores. Testing on the vignette example, but using all the transcripts, the one-sample z-score method takes < 20 seconds while the signed rank method takes > 200 seconds (12x speedup), while they have a high rate of agreement on the detected set (30:1 in common vs discordant).
• Removed the fast=0 methods that were previously implemented where ranks could optionally be recomputed for every permutation. This was much slower and didn’t have any appreciable benefit.
• readEDS() has moved to the eds package, such that fishpond no longer requires Rcpp and C++ code compilation.

• Fix bug identified by GitHub user @JosephLalli, where importAllelicCounts would find a1 and a2 strings internal to gene IDs, instead of at the suffix.

                   Changes in version 2.3.22                        
  

• Fix bug identified by GitHub user @JosephLalli, where importAllelicCounts would find a1 and a2 strings internal to gene IDs, instead of at the suffix.

                   Changes in version 2.3.14                        
  

• For simple paired swish analysis, adding a fast=1 method which uses a one-sample z-score on the paired LFCs (averaged over samples, then median over inferential replicates). The permutation is computed by changing the signs of the LFC matrix and recomputing z-scores. Testing on the vignette example, but using all the transcripts, the one-sample z-score method takes <20 seconds while the signed rank method takes >200 seconds (12x speedup), while they have a high rate of agreement on the detected set ( 30:1 in common vs discordant).

• Removed the fast=0 methods that were previously implemented where ranks could optionally be recomputed for every permutation. This was much slower and didn’t have any appreciable benefit.

                    Changes in version 2.3.7                        
  

• readEDS() has moved to the eds package.

FlowSOM

                    Changes in version 2.5.6                        

• Reversed PlotDimred back to scattermore instead of geom_hex. Uses geom_point if scattermore is not available.

• Added support for custom colors and limits in PlotDimRed

                    Changes in version 2.5.5                        
  

• AddAnnotation now works correctly after using UpdateMetaclusters. The function also works slightly different. See examples.

• Fixed issue with wrong coloring in PlotDimRed

                    Changes in version 2.5.4                        
  

• percentage_positives in GetFeatures now works with a FlowSOM with updated metacluster labels

                    Changes in version 2.5.3                        
  

• Bugfix in GetChannels

                    Changes in version 2.5.2                        
  

• Bugfixes to pass BioConductor check

• Bugfixes in Plot2DScatters: when ggpointdensity is not installed, normal ggplot colors are used

• ParseNodeSize is now exported

                    Changes in version 2.5.1                        
  

• Version bump to get the same version as on BioConductor

• Changed yMargin parameter in PlotFileScatters to yLim for consistency

• Added possibility to use abbrevations in GetFeatures, GetCounts, GetPercentages, PlotFileScatters, PlotDimRed, ParseQuery, Plot2DScatters and PlotNumbers

• Moved UpdateFlowSOM to 0_FlowSOM.R

• Changed examples in PlotFlowSOM, PlotVariable and PlotStars

• Fixed issues from check: deleted examples with GetFlowJoLabels and used a csv instead, changed geom_scattermore to geom_hex for less dependencies. Moved packages to Suggest instead of Import.

• ParseNodeSize is now exported

flowSpecs

              Changes in version 1.11 (2022-07-23)                  

• Updating the specMatCalc function, to allow for inclusion of samples with an internal negative control.

• Removing the dependency hexbin, as it is not in use (ggplot2 since 1.9.3)

fmrs

                    Changes in version 2.0.0                        

IMPROVEMENTS SINCE LAST RELEASE

• The package is rewritten using .Call function.
• The codes for Weibull distribution are improved.

BUG FIXES

• Several bugs are fixed which caused the results to be different for the same analysis.

FRASER

                    Changes in version 1.8.1                        

• Bugfix in merging splicing counts (#41)

gage

                   Changes in version 2.47.1                        

• korg now include 8282 KEGG species or 1449 new species beyond 2020.

• updated khier to included newly added reference pathways. kegg.gsets can work with 477 pathways now.

gdsfmt

                   Changes in version 1.34.0                        

UTILITIES

• update the web links

GeneNetworkBuilder

                   Changes in version 1.39.2                        

• Add subsetNetwork function.

                   Changes in version 1.39.1                        
  

• Add unrooted network.

• Add sample code for subset graph.

GeneTonic

                    Changes in version 2.2.0                        

New features

• gs_heatmap gains the winsorize_threshold parameter, to control the behavior of the geneset heatmap in presence of extreme values, either negative or positive ones. If not specified, the heatmap is not introducing any winsorization.
• map2color() has a behavior that better accounts for asymmetric ranges of values. This propagates to some of the functions that use it for mapping to colors, such as enrichment_map(), or ggs_backbone().

Other notes

• Fixed the behavior of the reactive elements after uploading the GeneTonicList object at runtime.
• Fixed the label namings for the gs_heatmap function
• The enhance_table() function can handle the case where a gene is in the enrichment results table but not present in the annotation (e.g. annotations are updated, so some correspondences might get lost). It also presents an informative message on which genesets/genes are potentially responsible for the behavior.
• Some additional checks are in place for controlling the cases where the z_score of a geneset is detected as NA (e.g. because there was a mismatch between gene names and identifiers in the annotation).

GenomeInfoDb

                   Changes in version 1.34.0                        

NEW FEATURES

• Add update() method for Seqinfo() objects. See ‘?Seqinfo’.

• Implement getChromInfoFromUCSC() “offline mode” for a selection of genomes. See ‘?getChromInfoFromUCSC’.

• Register the following NCBI assemblies:
  • a few Triticum aestivum assemblies (bread wheat)
  • a Pteropus alecto assembly
  • an Eucalyptus grandis assembly
  • a few Plasmodium falciparum assemblies (malaria parasite)
  • the Dog10K_Boxer_Tasha assembly
  • the Felis_catus_9.0 assembly
  • the UCB_Xtro_10.0 assembly

• Register the following UCSC genomes: equCab1, equCab2, equCab3, mpxvRivers, hs1, canFam6, felCat9, xenTro10.

• Export and document find_NCBI_assembly_ftp_dir().

DEPRECATED AND DEFUNCT

• Remove releaseName() method for GenomeDescription objects. The releaseName() method for GenomeDescription objects was deprecated in Bioconductor 3.12 and defunct in Bioconductor 3.15. Also move the releaseName() generic function to the BSgenome package.

GenomicAlignments

                   Changes in version 1.34.0                        

BUG FIXES

• Fix buffer overflow in cigarNarrow()/cigarQNarrow() See commit 5d0a29b2795a95dfb006e8e54c7532b12bd5e79c.

GenomicFeatures

                   Changes in version 1.50.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Use useEnsemblGenomes() instead of useMart() wherever possible.

• Improve pcoverageByTranscript() implementation. The function now uses a chunking strategy to handle bigger CompressedGRangesList objects and to reduce memory footprint. Note that even with this improvement, the function is still not very efficient.

• Rename proteinToGenome() argument ‘txdb’ -> ‘db’.

BUG FIXES

• Change test for ‘circ_seqs’ argument in makeTxDbPackageFromUCSC() from an error to a warning if argument set to NULL.

GenomicFiles

                    Changes in version 1.34                         

BUG FIXES

• (v 1.33.1) reduceRanges() supports files as character vectors.

GenomicRanges

                   Changes in version 1.50.0                        

• No changes in this version.

GenomicScores

                   Changes in version 2.10.0                        

USER VISIBLE CHANGES

• Added two new score sets and corresponding metadata for mm39: phastCons35way.UCSC.mm39 and phyloP35way.UCSC.mm39.

• Added new method ‘wgscores()’ to find which genomic scores are present in a given set of genomic ranges. Feature request by https://github.com/rcastelo/GenomicScores/issues/20

• Improved error messages about optional arguments without name or with a mispecified name in the call to ‘gscores()’.

BUG FIXES

• Bugfix for parameters ‘ref’ and ‘alt’ when used with HDF5 backends.

GeomxTools

                    Changes in version 3.1.1                        

• Documentation correction

                    Changes in version 3.1.0                        
  

• No changes from 2.99.2

ggmsa

                    Changes in version 1.3.3                        

• calling \dontrun{} for examples on ggmsa()

                    Changes in version 1.3.2                        
  

• bugfix: geom_msaBar conservation layer incorrectly aligned issues#34(2022-5-13, Fri)

                    Changes in version 1.3.1                        
  

• A new feature–selects ancestral sequence on Tree-MSA plot treeMSA_plot (2022-4-14, Thu)
• A new feature–visualization of genome alignment ggmaf (2022-4-14, Thu)
• A test feature–visualization protein-protein interactive (2022-4-14, Thu)
• updated the way smooth is invoked on simplot(2022-01-03, Mon)

ggspavis

             Changes in version 1.3.1 (2022-10-11)                  

• support for multiple-sample datasets

ggtree

                    Changes in version 3.6.0                        

• Bioconductor RELEASE_3_16 (2022-11-02, Wed)

                    Changes in version 3.5.3                        
  

• add new citation (the iMeta 2022 paper) (2022-09-26, Mon)
• move scale_color_subtree() to the ‘ggtreeDendro’ package (2022-09-23, Fri)
• update fortify method for pvclust object (2022-08-15, Mon)

• add citation of the tree data book (2022-08-13, Sat)

                    Changes in version 3.5.2                        
  

• scale_color_subtree() now supports passing a numeric value and internally it will call cutree(tree, k) (2022-08-11, Thu)
• support ‘linkage’ class defined in the ‘mdendro’ package (2022-08-11, Thu)
• clone the plot environment before assigning layout (2022-07-19, Tue, #516)
• bug fixed in ‘equal_angle’ layout (2022-07-08, Fri, #514)

• optimize geom_tiplab to better compatible with dendrogram layout (2022-06-23, Thu, #508)

                    Changes in version 3.5.1                        
  

• as.phylo.hclust2 to correct edge length as displayed in stats:::plot.hclust (2022-06-21, Tue)
• add outline to nodepies (2022-06-20, Mon, #506)
• new ‘slanted’ layout for branch.length = ‘none’ (2022-04-29, Fri, #497)
• only works for Cartesian coordination, that means it will not work for layout = ‘radial’

ggtreeExtra

                    Changes in version 1.7.1                        

• fix a bug of subset data (when the value mapped to x aesthetic contains negative value.)

• fix a bug when x of mapping in data is only one unique.

• https://github.com/YuLab-SMU/ggtreeExtra/issues/24

glmGamPoi

                     Changes in version 1.9                         

• Breaking change to the way that non-standard evaluation parameters are handled. Variables in arguments such as ‘pseudobulk_by’ or ‘subset_to’ which evaluate to a single string are no longer interpreted as referring to a column. This change makes the handling of NSE more consistent.

• Add new function ‘pseudobulk_sce’ to easily form pseudobulk samples

GOSemSim

                   Changes in version 2.23.1                        

• Replacing DO.db with HDO.db (2022-07-29, Mon)

GRaNIE

             Changes in version 1.1.21 (2022-12-13)                 

Major changes

• major object changes and optimizations, particularly related to storing the count matrices in an optimized and simpler format. In short, the count matrices are now stored either as normal or sparse matrices, depending on the amount of zeros present. In addition, only the counts after normalization are saved, the raw counts before applying normalization are not stored anymore. If no normalization is wished by the user, as before, the “normalized” counts are equal to the raw counts. GRaNIE is now more readily applicable for larger analyses and single-cell analysis even though we just started actively optimizing for it, so we cannot yet recommend applying our framework in a single-cell manner. Older GRN objects are automatically changed internally when executing the major functions upon the first invocation.
• various Documentation and R help updates
• the function generateStatsSummary now doesnt alter the stored filtered connections in the object anymore. This makes its usage more intuitive and it can be used anywhere in the workflow.
• removed redundant biomaRt calls in the code. This saves time and makes the code less vulnerable to timeout issues caused by remote services
• due to the changes described above, the function plotPCA_all now can only plot the normalized counts and not the raw counts anymore (except when no normalization is wanted)
• the GO enrichments are now also storing, for each GO term, the ENSEMBL IDs of the genes that were found in the foreground. This facilitates further exploration of the enrichment results.

Minor changes

• many small changes in the code

             Changes in version 1.1.13 (2022-09-13)                 
  

Major changes

• many Documentation and R help updates, the Package Details Vignette is online
• The workflow vignette is now improved: better figure resolution, figure aspect ratios are optimized, and a few other changes
• the eGRN graph structure as built by build_eGRN_graph() in the GRaNIE object is now reset whenever the function filterGRNAndConnectGenes() is successfully executed to make sure that enrichment functions etc are not using an outdated graph structure.
• the landing page of the website has been extended and overhauled
• removed some dependency packages and moved others into Suggests to lower the installation burden of the package. In addition, removed topGO from the Depends section (now in Suggests) and removed tidyverse altogether (before in Depends). Detailed explanations when and how the packages listed under Suggests are needed can now be found in the new Package Details Vignette and are clearly given to the user when executing the respective functions
• major updates to the function getGRNConnections, which now has more arguments allowing a more fine-tuned and rich retrieval of eGRN connections, features and feature metadata
• a new function add_featureVariation to quantify and interpret multiple sources of biological and technical variation for features (TFs, peaks, and genes) in a GRN object, see the R help for more information
• filterGRNAndConnectGenes now doesnt include feature metadata columns to save space in the result data frame that is created. The help has been updated to make clear that getGRNConnections includes these features now.

Minor changes

• small changes in the GRN object structure, moved GRN@data$TFs@translationTable to GRN@annotation@TFs. All exported functions run automatically a small helper function to make this change for any GRN object automatically to adapt to the new structure
• many small changes in the code, updated argument checking, and preparing rigorous unit test inclusion

• internally renaming the (recently changed / renamed) gene type lncRNA from biomaRt to lincRNA to be compatible with older versions of GRaNIE

              Changes in version 1.1 (2022-05-31)                   
  

Minor changes

• added the argument maxWidth_nchar_plot to all functions that plot enrichments, and changed the default from 100 to 50.

Bug fixes

• fixed a small bug that resulted in the enrichment plots to ignore the value of maxWidth_nchar_plot

graphite

             Changes in version 1.43.2 (2022-10-31)                 

• Updated all pathway data.

GreyListChIP

                   Changes in version 1.29.1                        

• Change maintainer email from Gord to Rory.

GSVA

                    Changes in version 1.46                         

BUG FIXES

• Bugfix for https://github.com/rcastelo/GSVA/issues/61 to enable using the ssgsea method with one single column (sample) in the input data container.

• Bugfix when input is a SummarizedExperiment and assays contain a data.frame instead of a matrix.

HDF5Array

                   Changes in version 1.26.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Try harder to find and load the matrix rownames of a 10x Genomics dataset. See commit abafbb9e99ad54a64e5013305486b97daa9442bc.

BUG FIXES

• Handle HDF5 sparse matrices where shape is not an integer vector. When the shape returned by internal helper .read_h5sparse_dim() is a double vector it is now coerced to an integer vector. Integer overflows resulting from this coercion trigger an error with an informative error message. See GitHub issue #48.

hermes

                    Changes in version 1.0.1                        

• Additional version argument for connect_biomart to specify an Ensembl version.
• Fixed tests.

Herper

                    Changes in version 1.6.1                        

• Added vignette describing how to work with Herper on machines with old GCC compilers

• Added additonal messaging and control of messaging

• Fixed bug that causes error on new miniconda install when path is abbreviated with ‘~’

HIBAG

                   Changes in version 1.34.0                        

• fix the compiler issue on Mac M1 chip

• fix the C stack error in RStudio

HiCDCPlus

             Changes in version 1.5.2 (2022-06-06)                  

• Fixed bug that prevented juicer to setup

             Changes in version 1.5.1 (2022-05-08)                  
  

• Updated references to juicer

hipathia

             Changes in version 2.13.1 (2022-07-27)                 

• Fixing bug in nodes DE with limma with high rates of 0-variance genes.

HPAanalyze

                    Changes in version 1.15                         

• Changes in version 1.15.1
  • Update built-in data to HPA version 21.1.
• Changes in version 1.15.0
  • Starting devel for Bioconductor 3.16

IgGeneUsage

         Changes in version 1.11.2-1.11.11 (2022-10-24)             

• man files updated

• vignette updated

• d_zibb data and inst/scripts/d_zibb.R added: simulated data from zero-inflated beta-binomial (ZIBB) distribution

• minor fixes, function clarity/readibility improved

• probe compilation errors on Windows

• stanmodels used properly in v. 1.11.10, no extra compilation

• stanmodels in tests/ fixed, no extra compilation

illuminaio

             Changes in version 0.41.0 (2022-11-01)                 

• The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.17 for R-devel.

             Changes in version 0.40.0 (2022-11-01)                 
  

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.16 for R (>= 4.2.2).

             Changes in version 0.39.2 (2022-10-31)                 
  

Miscellaneous

• Fix NEWS.md version formatting.

             Changes in version 0.39.1 (2022-09-23)                 
  

Bug Fixes

• readIDAT() would only return the first five Unknown.N fields. Additional ones would be dropped.

• readIDAT() could produce Warning message: In readChar(con, nchars = n) : truncating string with embedded nuls if the IDAT file had an Unknown.6 field. Until we know what that field represents, it is parsed as an (nbytes, <byte sequence>) integer vector.

             Changes in version 0.39.0 (2022-04-26)                 
  

• The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.16 for R-devel.

imcRtools

             Changes in version 1.3.10 (2022-10-22)                 

• fix axis.ratio to 1 in plotSpatial function and set scales = “fixed”

             Changes in version 1.3.9 (2022-10-14)                  
  

• new function for spatial community detection

             Changes in version 1.3.8 (2022-10-13)                  
  

• exclude a single validity check to to class changes in the ggraph package

             Changes in version 1.3.7 (2022-08-11)                  
  

• new function to measure minimal distances to cells of interest

             Changes in version 1.3.6 (2022-07-28)                  
  

• new function to measure size of patch

             Changes in version 1.3.5 (2022-06-15)                  
  

• Added three spatial context functions

             Changes in version 1.3.4 (2022-06-14)                  
  

• Avoid duplicated columns when generating nodes for plotSpatial

             Changes in version 1.3.3 (2022-06-03)                  
  

• Bug fix: specify the number of nodes in patchDetection function

             Changes in version 1.3.2 (2022-05-30)                  
  

• Bug fix: avoid duplication of metadata entries

             Changes in version 1.3.1 (2022-04-28)                  
  

• Bug fix: avoid using factors in testInteraction function for group_by

immunoClust

                   Changes in version 1.29.2                        

• CHANGES

  • code cleaning

                   Changes in version 1.29.1                        
    

• CHANGES
  • minor code improvements

infercnv

             Changes in version 1.13.1 (2022-10-17)                 

• Updated how the Leiden subclustering is run to use igraph instead of the Python implementation called through reticulate, and to run a PCA before building neighboring graph.

• Added option to run a second round of subclustering that is per chromosome (for the HMM predictions).

• Added method that runs the i6 HMM predictions based on per chromosome subclustering.

• Add arguments/options for Leiden settings and change defaults.

• Change default analysis mode to subclusters.

• Fix plotting when no hclust is already stored in the object and have clusters with only 1 or 2 cells.

• Fix to add_to_seurat so that unsorted chromosomes that are only named by their number are read as character and not integers, which resulted in the named features using the unsorted index as a name.

• Allow adding a custom column prefix when using add_to_seurat (by @matt-sd-watson )

• Add an “assay_name” option to add_to_seurat in case the assay is not named “RNA” like expected.

• More helpful message displayed before erroring when trying to run add_to_seurat without having run the HMM.

• Add option to filter genes used in subclustering based on zscore.

• Fix i3 settings calculation.

• Change to not output “scaled” CNV proportion values when running the HMM in i3 mode as we don’t know if a gain/loss is of only 1 copy or more.

• Update actually used “levels” in the factor used to store gene chromosome information so that contigs entirely filtered out don’t mess up the color bars on the heatmap.

• Linked write_expr_matrix option in plot_cnv to the methods that plot the observations and references so that the split matrix also don’t get output when set to false.

• Fix for plot_cnv(plot_chr_scale=T) to handle chromosomes with a single gene on them, though such chromosomes should be dropped entirely.

InteractiveComplexHeatmap

                    Changes in version 1.5.1                        

• do_default_click_action and do_default_bruch_action are reset to FALSE if subHeatmapOutput() is not used.

IRanges

                   Changes in version 2.32.0                        

NEW FEATURES

• splitAsList() can now perform a “dumb split”, that is, when no split factor is supplied, ‘splitAsList(x)’ is equivalent to ‘unname(splitAsList(x, seq_along(x)))’ but is slightly more efficient.

SIGNIFICANT USER-VISIBLE CHANGES

• Add ellipsis argument (…) to the gaps() generic function.

ISAnalytics

             Changes in version 1.7.6 (2022-10-25)                  

• Fixed minor bugs and typos

             Changes in version 1.7.5 (2022-10-05)                  
  

• Fixed build issues

             Changes in version 1.7.4 (2022-10-04)                  
  

VISIBLE USER CHANGES

• Progress bars for long processing functions are now implemented via the package progressr, added a wrapper function for fast enabling progress bars, enable_progress_bars()
• Introduced logging for issues in HSC_population_size_estimate() - signals eventual problems in computing estimates and why

BUG FIXES AND MINOR CHANGES

• Fixed minor bugs and typos

             Changes in version 1.7.3 (2022-06-17)                  
  

BUG FIXES AND MINOR CHANGES

• All functions that check for options now have a default value if option is not set
• CIS_grubbs function is now faster (removed dependency from psych::describe)

NEW

• New functions CIS_grubbs_overtime() and associated plotting function top_cis_overtime_heatmap() to compute CIS_grubbs test over time

             Changes in version 1.7.2 (2022-05-23)                  
  

BUG FIXES AND MINOR CHANGES

• Fixed minor issues in import_association_file() - function had minor issues when importing *.xlsx files and missing optional columns threw errors
• Fixed bug in as_sparse_matrix() - function failed when trying to process an aggregated matrix

NEW

• Added 2 new utility functions export_ISA_settings() and import_ISA_settings() that allow a faster workflow setup

             Changes in version 1.7.1 (2022-05-04)                  
  

BUG FIXES AND MINOR CHANGES

• Fixed minor issue in compute_near_integrations() - function errored when report_path argument was set to NULL
• Fixed dplyr warning in integration_alluvial_plot() internals
• Fixed issue with report of VISPA2 stats - report failed due to minor error in rmd fragment
• Internals of remove_collisions() use again dplyr internally for joining and grouping operations - needed because of performance issues with data.table
• fisher_scatterplot() has 2 new arguments that allow the disabling of highlighting for some genes even if their p-value is under the threshold

iSEE

                   Changes in version 2.9.12                        

• Export constants used in iSEEu.

                   Changes in version 2.9.11                        
  

• Fix R CMD check warnings about missing documentation.

                   Changes in version 2.9.10                        
  

• Enable customisation of hovering tooltip in DotPlot panels including colData or rowData information.

                    Changes in version 2.9.9                        
  

• Allow screenshots in vignettes to use full width of pkgdown site.

                    Changes in version 2.9.8                        
  

• Enable autocompletion for feature names in the heatmap feature selection modal.

                    Changes in version 2.9.7                        
  

• Update FontAwesome icon question-circle to circle-question (v6).

                    Changes in version 2.9.6                        
  

• Bugfix related to https://github.com/rstudio/shiny/issues/3125, mainly applicable to custom landing pages that render a DT::datatable() prior to selectInput().

                    Changes in version 2.9.5                        
  

• Bugfix reverting a change in 2.9.3 breaking re-rendering of reactivated panels.

• Complete bugfix to prevent unnecessary re-rendering of ComplexHeatmapPlot panel when dimension of an incoming multiple selection is dismissed by the options of the child panel.

                    Changes in version 2.9.4                        
  

• Bugfix setting the active multi-selection info of Table panels to a fixed message, as the panel is not re-rendered when search boxes are used.

• Bugfix re-rendering ComplexHeatmapPlot panels when displaying incoming column selection.

                    Changes in version 2.9.3                        
  

• Partial bugfix avoiding re-rendering of ComplexHeatmapPlot panel when an incoming row selection changes if custom rows are in use. The partial bugfix only applies if the ComplexHeatmapPlot also disables the restriction on any incoming column selection.

                    Changes in version 2.9.2                        
  

• Document the existing panel modification modes.

                    Changes in version 2.9.1                        
  

• Add spinner to ComplexHeatmapPlot.

iSEEu

                    Changes in version 1.9.3                        

• Fix numbering issue affecting the coloring of LogFCLogFCPlot panels.

                    Changes in version 1.9.2                        
  

• Depend on the iSEEhex package to initiate the “iSEEverse”.

isomiRs

                   Changes in version 1.25.1                        

FIX

• remove DiscriMiner dependency and functions since it is not available for 3.16

kebabs

                   Changes in version 1.31.2                        

• changed dependency to ‘Matrix’ package (now requires at least version 1.5-0)

                   Changes in version 1.31.1                        
  

• minor changes in coercions in accordance with latest version of ‘Matrix’ package

                   Changes in version 1.31.0                        
  

• new branch for Bioconductor 3.16 devel

KEGGREST

                   Changes in version 1.37.0                        

BUG CORRECTION

• 1.37.1 Fixes new endpoint

• 1.37.2 http to https fixes windows error

limma

                   Changes in version 3.54.0                        

• New function goanaTrend() to estimate a covariate-dependent trend in the probability of differential expression for use in goana() and kegga() with trend=TRUE. The trend estimated by goanaTrend() is squeezed slightly towards constancy to provide stability when the number of DE genes is small. The amount of squeezing decreases with the number of DE genes.

goana() and kegga() now call goanaTrend() when the trend argument is used. When plot=TRUE the plot is now created by goanaTrend() instead of by barcodeplot().

• Rename argument prior.prob to null.prob in goana() and kegga().

• Update goana() and kegga() code to catch NA gene IDs or covariate values.

• goana() and kegga() no longer give an error when a trend is estimated but there are no DE genes.

• kegga() now uses https instead of http links when reading from rest.kegg.jp.

• Add new argument fc to topTable() and topTableF(). Change default for lfc to NULL instead of 0.

• lmFit() now checks explicitly for NAs in the design matrix.

• Update references listed on help pages to use DOIs instead of URLs.

MassSpecWavelet

             Changes in version 1.63.6 (2022-10-15)                 

• Fix regression in cwt() when scales has length 1.

             Changes in version 1.63.5 (2022-10-11)                 
  

• getRidge() supports a scaleToWinSize parameter. This argument controls how scales get mapped to window sizes. These windows are used to track the local maxima into ridges. MassSpecWavelet had a criteria of winsize <- 2*scale+1, while xcms modified it to winsize <- floor(scale/2). This new argument enables xcms maintainers to call MassSpecWavelet’s getRidge (if they want to) using their criteria, while it still lets us preserve backwards compatibility in our results. See ?getRidge for further details.

• The getLocalMaximumCWT() is_amp_thres_relative parameter is now isAmpThreshRelative, for consistency with other parameter capitalization in the package. Since it was introduced 10 days ago, I don’t think there will be more than one user using it.

• getLocalMaximumCWT() and peakDetectionCWT have a exclude0scaleAmpThresh parameter. When computing the relative amp.Th, if this parameter is set to TRUE, the amp.Th will exclude the zero-th scale from the max(wCoefs). The zero-th scale corresponds to the original signal, that may have a much larger baseline than the wavelet coefficients and can distort the threshold calculation. The default value is FALSE to preserve backwards compatibility.

• peakDetectionCWT lets the user pass custom arguments to getRidge().

             Changes in version 1.63.4 (2022-10-10)                 
  

• The improvements in localMaxima() and cwt() provide significant speed-ups to peakDetectionCWT() as well as better scalability.

• A prepareWavelets() function lets the user pre-compute the daughter wavelets for more efficient cwt() calculations when applied on multiple spectra. When used transforming 1000 spectra, of 2000 points long each, using 25 different scales, cwt() is twice as fast as in previous versions. Further improvements to avoid some memory allocations are still feasible in future versions.

• Through the prepareWavelets() function, we provide the extendLengthScales argument, that provides the same functionality than the extendLengthMSW argument in xcms:::MSW.cwt().

• The peakDetectionCWT() function accepts a prepared_wavelets object in the scales argument for better efficiency.

             Changes in version 1.63.3 (2022-10-10)                 
  

• localMaxima() has a more efficient implementation of the algorithm, now being 10x faster than before, while giving the same results.

• Experimentally, localMaxima() can use a new and different algorithm for detecting local maxima. See the new “Finding local maxima” vignette for further details.

             Changes in version 1.63.2 (2022-09-29)                 
  

• Let getLocalMaximumCWT() have a relative amp.Th. Related to #4.
• Fix bug on identifyMajorPeaks() where nearbyWinSize was forced to 150 if nearbyPeak was set to TRUE. Related to #4.

• Added excludeBoundariesSize argument to identifyMajorPeaks(). Before, nearbyWinSize was used for two different but related criteria: the range for including peaks close to a large peak AND the range to exclude peaks close to the beginning and end of the signal. Now, we have two independent arguments for each setting. The current behaviour does not change, but it is now more flexible. Related to #4.

             Changes in version 1.63.1 (2022-07-08)                 
  

• Drop sav.gol alias from the documentation. Related to #2
• Explain how the scales argument is defined in relation to the mother wavelet.
• Add sessionInfo() to the vignette

MatrixGenerics

                    Changes in version 1.9.1                        

• Fix for functions whose first argument is not x (https://github.com/Bioconductor/MatrixGenerics/issues/28 and https://github.com/Bioconductor/MatrixGenerics/pull/29).

MatrixQCvis

             Changes in version 1.5.9 (2022-10-19)                  

• add ShinyApps to biocViews

             Changes in version 1.5.8 (2022-09-30)                  
  

• replace vegan::metaMDS by MASS::isoMDS for NMDS dimension reduction

             Changes in version 1.5.7 (2022-09-29)                  
  

• change renderUI functions to update…Input whenever possible

• remove the dual interface for measured/missing values help pages in the values tab

• improve the formula/expression checks in the DE tab using the model.matrix and makeContrasts functions

             Changes in version 1.5.6 (2022-09-23)                  
  

• speed up non-server functions

             Changes in version 1.5.5 (2022-08-23)                  
  

• add unit tests for imputation of missing values

• bug fix (ncol instead of nrow) for calculation of BPCA imputation

             Changes in version 1.5.4 (2022-08-18)                  
  

• improve the imputation of missing values

             Changes in version 1.5.3 (2022-08-01)                  
  

• only use a subset of maximum 5000 features in the calculation of Hoeffding’s D values. In case there are less than 10000 features in the SummarizedExperiment object, all features of the SummarizedExperiment are taken

• createBoxplot precalculates the values of the boxplot instead on relying on geom_boxplot for calculation of the statistics

             Changes in version 1.5.2 (2022-07-20)                  
  

• remove the functions biocrates, maxQuant, and spectronaut from MatrixQCvis and move to the MatrixQCUtils package

             Changes in version 1.5.1 (2022-07-18)                  
  

• load package MatrixQCvis in report_qc.Rmd

matter

             Changes in version 1.99.2 (2022-10-31)                 

BUG FIXES

• Fix ‘chunkApply()’ behavior for when nchunks == 1

• Fix ‘atoms’ failure when ‘source’ is a compressed ‘drle’

• Properly ignore missing groups in ‘rowsweep()’ and ‘colsweep()’

             Changes in version 1.99.1 (2022-10-30)                 
  

BUG FIXES

• Minor bug fixes to ‘matter_list’ and ‘struct()’ behavior

• Minor bug fix to endomorphic subsetting of sparse matrices

• Minor bug fix to ‘binvec()’ behavior at vector endpoints

             Changes in version 1.99.0 (2022-10-23)                 
  

NEW FEATURES

• Complete re-implementation of sparse array code in C++

• Complete re-implementation of matter object C++ backends

• New ‘sparse_arr’ class with ‘sparse_mat’ and ‘sparse_vec’

• New ‘matter_arr’ class with ‘matter_mat’ and ‘matter_vec’

• New ‘asearch()’ function for approximate search with interpolation

• New ‘chunkApply()’ function replacing ‘chunk_apply()’, etc.

• New ‘colsweep()’ and ‘rowsweep()’ functions w/ group parameter

• New ‘colscale()’ and ‘rowscale()’ functions w/ group parameter

• New ‘drle_fct’ class for delta-run-length encoded factors

• New interpolation options for ‘sparse_arr’ objects

• Simplified deferred arithmetic operations interface

SIGNIFICANT USER-VISIBLE CHANGES

• New simplified constructors for most matter objects

• Updated S4 internals for most matter objects

• Updated S4 internals for sparse array objects

• Deprecated some rarely-used functions and classes

• Deprecated some S4 generic conflicts with core BioC packages

BUG FIXES

• Fix to ‘stream_var’ and ‘stream_sd’ behavior when n=0 or n=1

memes

                    Changes in version 1.5.2                        

• added a warning in runFimo in case bfile argument matches an existing local file.

                    Changes in version 1.4.1                        
  

• added an informative error message during importMeme when parse_genomic_coords fails with custom fasta import.

metabCombiner

                    Changes in version 1.7.1                        

• Addition of filtered features to metabData objects and filtered method

• Bug Fix in metabData():
  • zero values now treated as missing in Q calculations (zero = TRUE)
• Bug Fix in calcScores()/ evaluateParams():
  • rtrange calculations now account for missing values
• Bug Fix in reduceTable()/ reduceTableParam():
  • method argument included with “mzrt” option
• small logic fix in labelRows() / reduceTable()
  • previous version caused duplicate feature matches in rare cases

MetaboAnnotation

                     Changes in version 1.1                         

Changes in 1.1.6

• scoreVariables function to return the names of the score variables in a Matched object.

Changes in 1.1.5

• Fix issues on BioC build machines.

Changes in 1.1.4

• matchSpectra: support a CompDb with parameter target.
• Add CompAnnotionSource classes to support definition of references to annotation resources.
• Add CompDbSource class defining a reference to a CompDb database.
• matchSpectra: support for CompDbSource with parameter target.

Changes in 1.1.3

• Extend filterMatches framework (issue #86). ScoreThresholdParam added to perform filtering the matches based on a threshold for the scores.

Changes in 1.1.2

• lapply and endoapply methods (issue #84). lapply allows to apply any function to each subset of matches for each query element and returns the corresponding list of results. endoapply is similar but applies a function returning a Matched and returns a Matched representing updated matches.

Changes in 1.1.1

• Extend filterMatches framework (issue #81). SelectMatchesParam and TopRankedMatchesParam added to perform respectively manual filtering and keeping only the best ranked matches for each query element.

MetaboCoreUtils

                     Changes in version 1.5                         

MetaboCoreUtils 1.5.2

• substractElements drops elements with zero counts (issue #57).

MetaboCoreUtils 1.5.1

• Add functions formula2mz, adductFormula and multiplyElements (issue #55).

MetCirc

             Changes in version 1.27.2 (2022-10-19)                 

• use Spectra from Spectra for spectral representation instead of MSpectra from MSnbase

• remove compare_Spectra and normalizeddotproduct functions and use compareSpectra from Spectra package

• change vignette from Rnw to Rmd

             Changes in version 1.27.1 (2022-10-12)                 
  

• add ShinyApps in biocViews

MetNet

             Changes in version 1.15.2 (2022-05-18)                 

• improve documentation for function correlation and statistical and include information that also ggm can be used

             Changes in version 1.15.1 (2022-04-27)                 
  

• set ci in corr.test to FALSE to speed up calculation of correlation values (function correlation)

mia

                     Changes in version 1.5                         

• Added HintikkaXOData

• Added sample metadata option to getExperimentCrossAssociation

• estimateFaith: add support for multiple rowTrees

• calculateRDA/CCA: added variable argument & replaced altexp argument with altExp

• getExpCrossCorr: bugfix; samples should match when correlations between features are calculated

• getExpCrossCorr: Kendall’s tau is the default method

• mergeSEs: bugfix; links between trees and rows/cols were wrong & rowData did not include all info

• calculateDPCoA, calculateUnifrac & merge: add support for multiple trees

• altExp parameter to altexp

• agglomerateByRank: make rownames unique by default

• removed calculateDistance and calculateUniFrac alias

miaViz

                     Changes in version 1.5                         

• plot*Tree & *TreeData: Add support for multiple trees

• plot*Tree layout bugfix

microbiomeExplorer

                    Changes in version 1.7.1                        

• removed ZILN method as metagenomeSeq’s fitFeatureModel runs into issue with changed approach to compare ncol and nrow in limma’s lmFit

• cast matrixes into data.frame before calling lmFit to circumvent identical check for ncol & nrow in lmFit (if dimensions are named, results are equal, but not identical)

microbiomeMarker

                    Changes in version 1.3.2                        

• fix error on subgroup in lefse, #62, #55

             Changes in version 1.3.1 (2022-05-26)                  
  

• Development version on Bioconductor.

             Changes in version 1.2.1 (2022-05-26)                  
  

• Confounder analysis.
• Comparison of different methods.

MicrobiotaProcess

                    Changes in version 1.9.5                        

• fix the color of mp_plot_diff_boxplot and update mp_plot_abundance. (2022-10-27, Thu)

                    Changes in version 1.9.4                        
  

• keep the consistent color between the panels of mp_plot_diff_boxplot. (2022-10-18, Tue)
• optimizing the import of dtplyr. (2022-10-14, Fri)
• update mp_plot_diff_res to support the custom DAA results. (2022-09-27, Tue)
• update show method of MPSE to avoid the colname advice. (2022-09-27, Tue)
• add mp_dmn, mp_dmngroup, mp_divergence and update mp_plot_diff_boxplot, mp_plot_diff_cladogram to support the custom style. (2022-09-25, Sun)
• update mp_cal_dist to support specifying distmethod to a function. (2022-09-20, Tue)

• update left_join to support joining the dist class. (2022-09-20, Tue)

                    Changes in version 1.9.3                        
  

• fix a bug of mp_plot_diff_boxplot when taxatree slot is NULL. (2022-08-22, Mon)

                    Changes in version 1.9.2                        
  

• fixed the local vignettes. (2022-07-06, Wed)
• add mp_import_biom to build MPSE class from biom-format file. (2022-07-13, Wed)

• add ‘mp_plot_diff_boxplot’ to replace ggdiffbox. (2022-07-29, Fri)

                    Changes in version 1.9.1                        
  

• fix the color of legend in mp_plot_diff_cladogram. (2022-05-25)
• add mp_plot_diff_cladogram in vignetters. (2022-05-14)
• fixed a bug when the total counts of sample is less than chunks in mp_plot_rarecurve. (2022-05-14)
• add rm.zero argument in mp_plot_abundance to control whether mask the zero abundance of species. (2022-05-06)
• add taxa.class argument in mp_diff_analysis to test the specified taxa level. (2022-04-28)

midasHLA

                    Changes in version 1.5.2                        

• alleles and KIR frequenceis updated.

• failed test fixed after update in tide dependence.

minfi

                    Changes in version 1.43                         

• v1.43.1 Tightened the recognition code for 27k data to avoid conflict with the next release of the Allergy and Asthma array.

miRspongeR

                 Changes in version 2.1.1-2.1.3                     

• Add new reference and fix bug <2022-09-22, Thur>.

mirTarRnaSeq

             Changes in version 1.5.1 (2022-07-21)                  

• added stickers and README.md file

mistyR

                     Changes in version 1.5                         

• Added different modeling functions. Might not be completely backwards compatible!

Modstrings

             Changes in version 1.13.1 (2022-08-13)                 

• fixed bug in combineIntoModstrings

monaLisa

                    Changes in version 1.3.1                        

• update citation information

motifStack

                   Changes in version 1.41.1                        

• Fix the issue of importMatrix for mixed cases of alphabet in MEME format.

msa

                   Changes in version 1.29.3                        

• fix for possibly malformed inputs: all sequences are forced to uppercase characters (previously, ClustalW and ClustalOmega produced wrong results when called with lowercase sequences)

                   Changes in version 1.29.2                        
  

• fix in texshade.sty as suggested on TeXshade homepage at CTAN

                   Changes in version 1.29.1                        
  

• fix in argtable library (ClustalOmega) to avoid compilation errors on newest Mac OS

                   Changes in version 1.29.0                        
  

• new branch for Bioconductor 3.16 devel

MSA2dist

             Changes in version 1.1.7 (2022-10-05)                  

Major changes

• changed licence into GPL-3 to account for KaKs Calculator 2.0 licence

Minor improvements and bug fixes

             Changes in version 1.1.6 (2022-09-22)                  

Major changes

Minor improvements and bug fixes

• changed test-rcpp_KaKs

             Changes in version 1.1.5 (2022-09-19)                  
  

Major changes

Minor improvements and bug fixes

• changed rcpp_KaKs data access from data.frame to list

             Changes in version 1.1.4 (2022-07-16)                  
  

Major changes

Minor improvements and bug fixes

• fixed rcpp Warnings

             Changes in version 1.1.3 (2022-07-11)                  
  

Major changes

Minor improvements and bug fixes

• fixed rcpp indentation Warnings

             Changes in version 1.1.2 (2022-07-05)                  
  

Major changes

• Added KaKs Calculator 2.0 models as rcpp implementation

Minor improvements and bug fixes

• fixed some typos

             Changes in version 1.1.1 (2022-06-30)                  
  

Major changes

Minor improvements and bug fixes

• Added cds2codonaln

MsBackendMgf

                     Changes in version 1.5                         

Changes in 1.5.1

• Fix export method to fail if one or more columns contain either S4 classes or list-like structures.

MsCoreUtils

                     Changes in version 1.9                         

MsCoreUtils 1.9.2

• feat: imputation is compatible with HDF5Matrix objects
• feat: normalization is compatible with HDF5Matrix objects
• feat: matrix aggregation is compatible with HDF5Matrix objects
• fix+feat: aggregate_by_matrix now correctly handles missing data and implements ‘na.rm’
• Fix rla/rowRla man page.

MsCoreUtils 1.9.1

• Random forest imputation (using missForest) is now available (`method = “RF”)

MsCoreUtils 1.9.0

• New Bioc devel version

msImpute

                    Changes in version 1.7.1                        

• add width and shift params of the gaussian distribution in the down-shift mode of msImpute to provide more control over the shape of the distribution when observed peptides have high average expression and missing is group-specific.

mslp

                   Changes in version 0.99.6                        

NEW FEATURES

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

FIXES

• Added unit test for comp_slp and corr_slp.

• Updated vignette.

• Various fixes to reviewers questions.

MSnbase

                    Changes in version 2.23                         

Changes in 2.23.2

• Fix robust aggregation for MsCoreUtils 1.9.2.

Changes in 2.23.1

• Import spectrapply generic from ProtGenerics.

Changes in 2.23.0

• New release (Bioc 3.16)

msqrob2

                    Changes in version 1.5.3                        

• Added the option to use mixed models without ridge regression

• Added the option to use rowdata variables in the mixed models

                    Changes in version 1.5.1                        
  

• Fix weighted variance covariance matrix and QR decomposition in the msqrobLmer function

MSstatsTMT

             Changes in version 2.4.1 (2022-09-12)                  

• Minor change: fix the bug of data table in performing local normalization

MultiAssayExperiment

                   Changes in version 1.24.0                        

New features

• replicates provides the actual colnames identified as replicate observations for a particular biological unit in the sampleMap

Bug fixes and minor improvements

• Added an assay<- replacement method for robustifying saveHDF5MultiAssayExperiment with plain matrices
• Use BiocBaseUtils::setSlots and avoid warnings of triple colon use.
• Resolve issue when colData has one column when merging two MultiAssayExperiment objects, i.e., using the c method (@cvanderaa, #315)
• Increase efficiency in colnames and rownames methods (@cvanderaa, #314)
• Make ‘prefix’ inputs consistent in saveHDF5MultiAssayExperiment and loadHDF5MultiAssayExperiment (@asiyeka, #313)
• Improve performance for replicated method
• Update wideFormat documentation, when replicates present additional sets of columns will be appended to the produced DataFrame (@DarioS, #312)

MungeSumstats

                   Changes in version 1.5.18                        

Bug fix

• GHA fix.

                   Changes in version 1.5.17                        
  

New features

• By default ES taken as BETA new parameter added so users can specify if this isn’t the case (es_is_beta). If set to FALSE, mapping removed.

• Imputing BETA ordering has been changed so log(OR) will be sued before calculating from Z, SE.

                   Changes in version 1.5.16                        
  

New features

• A new method for computing the Z-score of a sumstats (compute_z input) has been added: BETA/SE. To use it set compute_z = ‘BETA’ to continue to use the P-value calculation use compute_z = ‘P’. Note the default is stil compute_z = FALSE.

Bug fix

• Remove erroneous print statement.

                   Changes in version 1.5.15                        
  

Bug fixes

• Fix NA representation for tabular outputs - By default, data.table::fread() leaves NAs blank instead of including a literal NA. That’s fine for CSVs and if the output is read in by fread, but it breaks other tools for TSVs and is hard to read. Updated that and added a message when the table is switched to uncompressed for indexing.

                   Changes in version 1.5.14                        
  

New features

• read_header:
• Can now read entire files by setting n=NULL.
• Improved reading in of VCF files (can read .vcf.bgz now).
• Now exported.
• Added unit tests.
• Remove seqminer from all code (too buggy).
• Automatically remove residual .tsv files after tabix indexing.
• import_sumstats:
• Use @inheritDotParams format_sumstats for better documentation.
• parse_logs: Added new fields.
• format_sumstats: Added time report at the end (minutes taken total). Since this is a message, will be included in the logs, and is now parsed by parse_logs and put into the column “time”.

Bug fixes

• index_tabular: Fixed by replacing seqminer with Rsamtools.
• When SNP ID’s passed with format 1:123456789, it will now be dealt with appropriately.

• compute_n can’t handle SNP level N values for imputation only population level. An explanatory error message has now been added.

                   Changes in version 1.5.13                        
  

Bug fixes

• Special characters causing issues with find empty columns function. Now fixed.

                   Changes in version 1.5.12                        
  

Bug fixes

• Mitchondrial (MT) SNPs’ chromosome value were being forced to NA by sort_coords function. This has been fixed.

                   Changes in version 1.5.11                        
  

Bug fixes

• Had to pass check_dups to other checks so they also wouldn’t be run. Now independent of non-biallelic check.

                   Changes in version 1.5.10                        
  

New features

• check_dups parameter added so duplicates won’t be removed if formatting QTL datasets

                    Changes in version 1.5.9                        
  

Bug fixes

• validate_parameters checks for incorrect version of dbSNP package, corrected.

                    Changes in version 1.5.6                        
  

Bug fixes

• MSS can now impute CHR, BP at a SNP level. For cases where CHR and/or BP are NA but the RS ID is present, these will now be imputed fromt he reference genome. Note previously, this imputation was done when the chr and/or bp column was missing.
• Print statement from liftover silenced when no liftover required
• check missing data function will no longer remove cases with NA’s in SNP_INFO column. The SNP_INFO column is created by MSS for cases with RS ID and some other information in the same SNP column (like rs1234:…..). Rather than throw out this info, it is stored in a new column - SNP_INFO. However, the remove missing data function was also looking in this column to remove SNPs. This has been corrected.
• find_sumstats():

• Fix N column in metadata.

                    Changes in version 1.5.5                        
  

New features

• save_format parameter created for format_sumstats. This will replace ldsc_format which is now deprecated. Use save_format=”LDSC” instead. Other options for save_format are generic standardised (NULL) and IEU Open GWAS VCF format (“openGWAS”).
• dbSNP version 155 has now been added. Users can now control the version of dbSNP to be used for imputation (144 or 155). Note that with the 9x more SNPs in dbSNP 155 vs 144, run times will increase.

Bug fixes

• Change where sex chromosomes were made lower case removed to match UCSC

                    Changes in version 1.5.4                        
  

New features

• Further mappings added

Bug fixes

• Duplication of non-bi-allelic and indels fixed

• Correct compute_nsize documentation

                    Changes in version 1.5.1                        
  

New features

• Export vcf2df.
• Move some post-processing function inside this function (e.g. drop duplicate cols/rows).
• read_vcf can now be parallised: splits query into chunks, imports them, and (optionally) converts them to data.table before rbinding them back into one object.
• Added report of VCF size (variants x samples) before processing to give user an idea of long it will take to process.
• Added arg mt_thresh to avoid using parallelisation when VCFs are small, due to the overhead outweighing the benefits in these cases.
• Added Linux installation instructions for axel downloader.
• Added 2nd tryCatch to downloader with different download.file parameters that may work better on certain machines.
• Avoid using file.path to specify URL in:
• get_chain_file
• import_sumstats
• Allow download_vcf to pass URLs directly (without downloading the files) when vcf_download=FALSE.
• download_vcf:
• Make timeout 10min instead of 30min.
• Make axel verbose.
• load_ref_genome_data:
• Give more informative messages that let user know which steps take a long time.
• Speed up substring preprocessing.
• read_vcf_genome: more robust way to get genome build from VCF.
• read_sumstats: Speed up by using remove_empty_cols(sampled_rows=), and only run for tabular file (read_vcf already does this internally).

Bug fixes

• select_vcf_field: Got rid of “REF col doesn’t exists” warning by omitting rowRanges.
• Ensured several unevaluated code chunks in vignettes/MungeSumstats.Rmd were surrounding by ticks.
• vcf2df: Accounted for scenarios where writeVcf accidentally converts geno data into redundant 3D matrices.
• Use data.table::rbindlist(fill=TRUE) to bind chunks back together.
• Remove unused functions after read_vcf upgrades:
• infer_vcf_sample_ids
• is_vcf_parsed
• check_tab_delimited
• read_vcf_data
• remove_nonstandard_vcf_cols
• Remove redundant dt_to_granges by merging functionality into to_granges.
• Adjusted liftover to accommodate the slight change.
• Fix is_tabix (I had incorrectly made path all lowercase).
• Let index_vcf recognize all compressed vcf suffixes.
• Add extra error handling when .gz is not actually bgz-compressed.

• Set BiocParallel registered threads back to 1 after read_vcf_parallel finishes, to avoid potential conflicts with downstream steps.

                    Changes in version 1.5.0                        
  

New features

• Added “query” column to find_sumstats output to keep track of search parameters.
• import_sumstats:
• Check if formatted file (save_path) exists before downloading to save time.
• Pass up force_new in additional to force_new_vcf.
• Updated Description tag in DESCRIPTION file to better reflect the scope of MungeSumstats.
• Upgraded read_vcf to be more robust.
• Edited Deps/Suggests
• Elevate IRanges to Imports.
• Remove stringr (no longer used)
• Add new internal function is_tabix to check whether a file is already tabix-indexed.
• read_sumstats:
• now takes samples as an arg.
• Parallises reading VCF using GenomicFiles.
• read_sumstats: now takes samples as an arg. By default, only uses first sample (if multiple are present in file).
• Remove INFO_filter= from ALS VCF examples in vignettes (no longer necessary now that INFO parsing has been corrected).
• download_vcf can now handle situations with vcf_url= is actually a local file (not remote).

Bug fixes

• AF (allele frequency) was accidentally being assigned as INFO column in VCFs where the INFO rows started with “AF”. This caused a large number of SNPs to be incorrectly dropped during the check_info_score step.
• If INFO score is not available, INFO column is now dropped entirely (rather than assigning all 1s).
• Adjusted test-vcf_formatting to reflect this. This avoids ambiguity about whether the INFO score is real or not.
• check_info_score:
• Added extra messages in various conditions where INFO is not used for filtering, and don’t add log_files$info_filter in these instances.
• Added unit tests.
• check_empty_cols was accidentally dropping more columns than it should have.
• Fix GHA pkgdown building:
• The newest version of git introduced bugs when building pkgdown sites from within Docker containers (e.g. via my Linux GHA workflow). Adjusting GHA to fix this.
• Fix write_sumstats when indexing VCF.
• Ensure read_sumstats can read in any VCF files (local/remote, indexed/non-indexed).
• Fix test-vcf_formatting.R
• line 51: had wrong AF value in string
• line 109: encountering error? due to duplicate SNPs?
• Fix test-check_impute_se_beta
• lines 51/52: setkey on SNP (now automatically renamed from ID by read_vcf).
• Fix test-read_sumstats:
• standardising of headers is now handled internally by read_sumstats.
• Ensure CHR is a character vector when being read in.
• line 44: Ensure extra cols in vcf_ss are dropped.
• parse_logs: Add lines to parsing subfunctions to allow handling of logs that don’t contain certain info (thus avoid warnings when creating the final data.table).
• ‘Avoid the use of ‘paste’ in condition signals’ fixed:
• check_pos_se
• check_signed_col
• Used to rely on gunzip to read bgz files, but apparently this functionality is no longer supported (possibly due to changes to how Rsamtools::bgzip does compression in Bioc 3.15. Switched to using fread + readLines in:
• read_header
• read_sumstats
• read_header: wasn’t reading in enough lines to get past the VCF header. Increase to readLines(n=1000).
• read_vcf: Would sometimes induce duplicate rows. Now only unique rows are used (after sample and columns filtering).
• Issue with mix of chr:bp:a1:a2 and chr:bp and rs id resolved

muscat

                   Changes in version 1.11.1                        

• bug fix in pbHeatmap(): previously failed for results from ‘mmDS()’

NanoMethViz

                    Changes in version 2.4.0                        

• Fixed plot_region_heatmap() producing the wrong plot when a factor is used for the chromosome.
• Fixed nanopolish and f5c import positions being off by 1.
• Fixed broken samples() setter for NanoMethResults.
• Added plot_agg_genes() function as a shorthand for plot_agg_regions(x, exons_to_genes(exons(x))).
• Added the ability to interrupt methy_to_bsseq() calls.
• Added handling for NanoMethResults objects in filter_methy(). If NanoMethResult is used as input, then NanoMethResult is invisibly returned as output.
• Added black outlines to exons in annotation to distinguish contiguous segments for features like tandem repeats.
• Added line_size argument to plot_gene(), plot_region() and plot_granges() plots for adjusting line size.
• Added subsample argument to heatmap plots, default 50. This reduces the number of rows shown the plot to the specified amount.
• Added get_exons_mm10(), get_exons_hg19(), and get_exons_hg38() as replacements for get_exons_mus_musculus() and get_exons_homo_sapiens().
• Changed heatmaps to no longer plot samples that are absent from sample annotations.
• Changed heatmap labels to appear on the right rather than on top.
• Changed heatmap alpha from 0.33 to 0.5.
• Changed arrows in exon connectors to appear in the middle as open arrow instead of at the end as closed arrow.
• Changed default X axis labels to be rescaled to appropriate SI-style. e.g. Kb, Mb, Gb.

NanoTube

                    Changes in version 1.3.7                        

• In addition to ruv::RUVIII, the RUVSeq::RUVg method can now be used for data normalization. Options have also been added to allow tuning of the parameters for these methods. More details are provided in the vignette.
• A csv or txt file containing a design matrix can be input as a ‘sampleTab’ in processNanostringData(). This facilitates easier differential expression analysis with more complex models, and an example has been added to the vignette.

• Various other improvements to vignette.

                    Changes in version 1.3.6                        
  

• NanoTube can now process zipped and tarred (.zip or .tar) directories, as well as gzipped (.gz) RCC files, such as those downloaded from GEO in many cases.

                    Changes in version 1.3.5                        
  

• Corrected a bug that caused NanoTube not to recognize reporters labeled as “Endogenous1”, “Endogenous2”, etc. as Endogenous.

ndexr

                   Changes in version 1.19.1                        

• UPDATE: Using the RCX package for working with networks. Defunct Functions:

• rcx_fromJSON: RCX::readJSON()

• rcx_toJSON: RCX::toCX()

• rcx_aspect_toJSON: rcx_aspect_toJSON

• rcx_new: RCX::createRCX()

• rcx_asNewNetwork: RCX::createRCX()

• rcx_updateMetaData: RCX::updateMetaData()

• print.RCX: RCX::print.RCX()

• rcx_toRCXgraph: RCX::toIgraph()

• rcxgraph_toRCX RCX::fromIgraph()

netZooR

                   Changes in version 1.1.12                        

• Reactivated unit tests for Ubuntu GitHub actions.
• LIONESS can now build single-sample coexpression networks using @kshutta’s implementation
• Fix for ALPACA singleton community case (detected by @talkhanz)
• Fix for CRANE significance test on constant modularity scores (detected by @talkhanz)
• Improved method description by @kshutta
• Fix for PANDA edge case when only expression is provided

ngsReports

                    Changes in version 2.0.0                        

• Added status bar to all plots from FastQC reports using pachwork

                   Changes in version 1.13.3                        
  

• Bug fix for importing macs2 logs

                   Changes in version 1.13.2                        
  

• Bug fix for importing DuplicationMetrics

                   Changes in version 1.13.1                        
  

• Bug fixes for importing macs2 logs

• Bug fixes for importing bowtie2 logs

nnSVG

             Changes in version 1.1.2 (2022-05-17)                  

• enable non-SpatialExperiment inputs

NxtIRFcore

             Changes in version 1.3.2 (2022-10-25)                  

• Announcing that NxtIRFcore will be superceded by SpliceWiz from Bioc 3.16 onwards.

             Changes in version 1.2.1 (2022-06-22)                  
  

• Bugfix for BuildReference: ignores “N” bases when translating codons (instead of returning an error)

• Bugfix for BuildReference: more versatile handling of cache locations for BiocFileCache

oncoscanR

                    Changes in version 1.1.0                        

• To simplify the workflow, the gender of the patient is not taken into account anymore. That implies that in a male sample, a gain of 3 extra copies on the X or Y chromosome is considered as a gain and not an amplification anymore. For female samples, nothing changes.
• The oncoscan coverage has been corrected to reflect only areas where there are groups of probes. Isolated probes where causing issues to identify arm-level alterations as ChAS segments where never extended to these probes and the 90% threshold could never be met (particularly on chromosomal arms 9p and Yq).

• Minor corrections in vignette

                    Changes in version 1.0.0                        
  

• The nLST test has been clinically validated on 384 patients from the PAOLA-1 trial and the recommended threshold is now >=15.
• The default value for arm-level alterations has been set to 90% as mentioned in the publication [Christinat et al., J Mol Diagn 2021; PMID: 34454110].
• The genomic LOH score (percent of LOH bases) has been added; score_gloh.
• Adds a flag “no tumor?” if the percentage of altered bases is less than 1%.

• Package to be released on Bioconductor

                    Changes in version 0.2.0                        
  

• Novel HRD score (nLST: number of LSTs, normalized by ploidy): score_nlst
• Change in Oncoscan workflow to use the nLST score and thresholds.
• New function to compute the number of Mb altered (with or without LOH): score_mbalt
• New function to compute the average copy number: score_avgcn
• New function to estimate the number of whole-genome duplication events (based on the average copy number and the thresholds defined by Carter et al.): score_estwgd

OncoSimulR

                     Changes in version 4.0                         

• MAJOR change: users can simulate interventions and adaptive therapy, as well as define, track, and use in fitness-dependent specifications user-defined variables.

• MAJOR change: users can specify birth and death rates as they want, including making both or just one frequency-dependent.

• onlyCancer = FALSE by default in all calls to oncoSimul*. This is a possible BRAEKING CHANGE.

• Plot fails with a meaningful error if simulations had unrecoverable exception or hit max wall time or max num tries.

• Improvements in vignette speed.

• Improvements in compilation speed.

            Changes in version 3.99.12 (2022-10-19)                 
  

• Try to allow vignette to build successfully in the ARM64 Mac build: use a try(plot) in chunk fdfmutex2.

• Use apa style citation and a few fixes to bib.

• Minor additions to vignette.

            Changes in version 3.99.11 (2022-10-13)                 
  

• Increase max.wall.time of two tests, as in very slow Windoze machines they can hit max wall time.

            Changes in version 3.99.10 (2022-10-13)                 
  

• onlyCancer = FALSE by default in all calls to oncoSimul*. This is a possible BRAEKING CHANGE.

• Plot fails with a meaningful error if simulations had unrecoverable exception or hit max wall time or max num tries.

• Faster vignette.

             Changes in version 3.99.9 (2022-09-30)                 
  

• Minor vignette split of code, to try to detect location of problem with ARM64 Mac build.

             Changes in version 3.99.8 (2022-09-15)                 
  

• Using “Unity builds” to decrease build (compilation) time; see file inst/miscell/README_Unity_compilation.

             Changes in version 3.99.7 (2022-09-13)                 
  

• Use c++14 and, in windows, do not use -O3: try to minimize build time.

             Changes in version 3.99.6 (2022-09-12)                 
  

• Udpated exprtk.

             Changes in version 3.99.5 (2022-07-19)                 
  

• Funding logo added to README.md and vignette.

             Changes in version 3.99.4 (2022-07-04)                 
  

• Failing a test in test.Z-intervention.R in Mac OS; did not fix correctly previous time.

             Changes in version 3.99.3 (2022-06-30)                 
  

• Failing a test in test.Z-intervention.R in Mac OS

             Changes in version 3.99.2 (2022-06-29)                 
  

• Vignette: author list and references.

             Changes in version 3.99.1 (2022-06-25)                 
  

• Users can specify birth and death rates as they want, including making both or just one frequency-dependent (thanks to Alberto González Klein).

• Interventions (thanks to Javier Muñoz Haro).

• User-defined variables and adaptive therapy (thanks to Javier López Cano).

orthogene

                    Changes in version 1.3.4                        

Bug fixes

• Remove Matrix.utils since it’s now deprecated.
• Reimplement the dMcast function as a new internal function within orthogene, since that’s the only function I use from Matrix.utils.

• Fix GHA workflow now that r-lib/actions@master has been removed.

                    Changes in version 1.3.3                        
  

Bug fixes

• Make test-map_orthologs_babelgene less stringent with the number of genes expected.

                    Changes in version 1.3.2                        
  

New features

• Add inst/grofiler_namespace.csv.gz for documentation purposes.

Bug fixes

• create_background:
• Ensure user-supplied bg gets used: https://github.com/neurogenomics/orthogene/issues/22

• Properly document internal data so that devtools::document doesn’t expect them to be exported objects.

                    Changes in version 1.3.1                        
  

New features

• plot_orthotree: Pass up tree_source arg.

                    Changes in version 1.3.0                        
  

New features

• aggregate_mapped_genes:
• Pass up additional args from map_genes.
• Add map_orthologs as a way to create gene_map automatically, when gene_map=NULL and input_species!=output_species.
• Split species into input_species and output_species args.
• Change method –> agg_method, and use method to pass to map_orthologs instead.
• Pass up additional args from map_orthologs.
• Add link to detailed explanation of matrix aggregation/expansion in many2many_rows docs.
• Automatically pick best method for many:1 or many:many mapping.
• as_integers: new arg that uses floor.
• Rename FUN to agg_fun.
• Add new data gprofiler_namespace. Used to validate target= arg in gprofiler2 functions.
• Upgraded aggregate_mapped_genes:
• Can now used gene_map made by map_orthologs or map_genes.
• Can now handle many:many relationships.
• Will automatically pick the best method to perform aggregation and/or expansion.
• Removed internal function aggregate_mapped_genes_twice
• Extracted aggregation args from non121_strategy and placed them in their own new own (agg_fun) since these options are no longer mutually exclusive due to many:many expansion/aggregation.
• Pass up as_DelayedArray
• Bump to v1.3.0 and R >=4.2 now that we’re developing on Bioc 3.16.
• Add ISSUE_TEMPLATE.
• prepare_tree:
• Add tree_source options: path / URL / OmaDB / UCSC / timetree

Bug fixes

• map_genes: Fix report at completion.
• Add safeguards against using aggregation when gene_df isn’t a matrix.
• Removed DelayedMatrixStats Import (no longer needed).
• Fix all unit tests and examples after making all updates.
• Recognize sparse/dense matrix or delayedarray in check_agg_args.

pathview

                   Changes in version 1.37.1                        

• fix bug in download.kegg caused by recent change in kegg rest API urls (http to https).

• korg now include 8282 KEGG species or 1449 new species beyond 2020.

peakPantheR

             Changes in version 1.11.1 (2022-08-05)                 

• Bugfix: manage mxML files without timestamp tag

pengls

                    Changes in version 1.3.2                        

• With predict function for cv.pengls objects

                    Changes in version 1.3.1                        
  

• Extend to MSE loss function
• Random fold splitting results in more even folds

phantasus

                   Changes in version 1.17.5                        

• All GEO datasets with <100K rows can be loaded

                   Changes in version 1.17.4                        
  

• Updated DESeq2 usage

PharmacoGx

                    Changes in version 3.1.4                        

• Modified downloadPSet function to automatically update the PharmacoSet class structure and resave the updated object after download
• This work around is necessary until we can rerun our data engineering pipelines to regenerate all of our PharmacoSet using the 3.1.0 package updates

• Added a number of additional methods for computing drug synergy metrics

                    Changes in version 3.1.1                        
  

3.1.0

• Update to slot names “cell” -> “sample” and “drug” -> “treatment”
• Update standardized identifier column names to match the above slot nomenclature: “cellid” -> “sampleid”, “drugid” -> “treatmentid”

PhyloProfile

                   Changes in version 1.10.3                        

• fixed bug parsing taxon names for input with more than 9999 taxa

                   Changes in version 1.10.1                        
  

• fixed bug button for tree uploading disappear #119

• improved parsing seq ID to create links for external DB #117

• fixed bug grepping domains for group comparison fn

• fixed bug parsing data for a list of input gene IDs #122

plotgardener

                    Changes in version 1.3.9                        

BUG FIXES

• Fixed vignette links in “Introduction to plotgardener” vignette.

                    Changes in version 1.3.7                        
  

BUG FIXES

• plotGenes and related functions will appropriately check for and handle custom OrgDbs.
• getExons will double-check for appropriate chromosome data to avoid incorrect plotting based on related chromosome contigs.

NEW FEATURES

• plotManhattan p-value data can be scaled according to a custom transformation, rather than being limited to -log10.

• plotRanges elements can be ordered randomly or by decreasing width before plotted row assignment.

                    Changes in version 1.3.6                        
  

BUG FIXES

• mapColors can appropriately map colors to a numeric vector with the same values, so long as a range is provided.

                    Changes in version 1.3.5                        
  

NEW FEATURES

• plotMultiSignal function can plot multiple signal track data sets in line with each other.
• calcSignalRange helper function will calculate an appropriate range for multiple signal data sets.
• pageLayoutRow and pageLayoutCol functions for generating row and column positions for a number of plot elements.

• Gene transcripts can be highlighted by gene name or transcript name with the parameter transcriptHighlights in plotTranscripts.

                    Changes in version 1.3.4                        
  

BUG FIXES

• plotPairsArches Bezier curve height calculations were fixed for pairs with different sized anchors.

                    Changes in version 1.3.3                        
  

NEW FEATURES

• plotSignal can now plot negative signal data alone or listed as a second file.

• A label parameter has been added for plotSignal for convenient labeling.

                    Changes in version 1.3.2                        
  

BUG FIXES

• plotSignal range parsing bug fixes were resolved.

• Note about double page rendering has been added to pageGuideHide() documentation.

                    Changes in version 1.3.1                        
  

• plotSignal bug fixes related to function not finding posSignal2 and negSignal2 variables with insufficient data.

• Documentation to introduction vignette has been added to explain double page rendering when using any removal function, particularly pageGuideHide().

                    Changes in version 1.3.0                        
  

Version bump for Bioconductor 3.15 release.

polyester

                   Changes in version 1.99.3                        

• NB function now exported

• note that version 1.99.3 on GitHub was version 1.1.0 on Bioconductor.

                   Changes in version 1.99.2                        
  

• bug fix in fragment generation (last 2 bases of transcript were never sequenced)

POMA

                   Changes in version 1.7.19                        

• New biocViews and Description
• Call external packages within each POMA function for consistency
• New methods: UMAP, PCR (Principal Components Regression), RNA-seq analysis (via DESeq2 package)
• Add different statistical methods in PomaVolcano()
• Estimate relative quality weights in PomaLimma()
• Update tests
• Update vignettes
• Several bug fixes

proDA

                    Changes in version 1.11                         

• Fix copy and paste bug that meant that the wrong value was used in the unregularized feature estimation procedure (see #18. Thanks to @amackey for spotting the bug).

pRoloc

                    Changes in version 1.37                         

Changes in version 1.37.1

• Fix bug in PerTubro classifiction function (see #146 and #147), contributed by mgerault.

pRolocGUI

                     Changes in version 2.7                         

CHANGES IN VERSION 2.7.2

• Explicitly add remap function for aggregation app

CHANGES IN VERSION 2.7.1

• Move LMB as maintainer
• Update URLs for Github repo
• Removed deprecated cogs icon to gears
• Fix bug in shinyhelper

CHANGES IN VERSION 2.7.0

• New version for Bioc 3.15

psichomics

                   Changes in version 1.24.0                        

• Bug fix: psichomics app now opens as expected instead of crashing

                   Changes in version 1.22.1                        
  

• Bug fix: GTEx data v8 can now be downloaded using newer versions of R
• Bug fix: UniProt REST API call now uses the updated API
• Bug fix: Updated deprecated setting to remove ggplot2 guide
• Documentation: Clarify how to get survival plots in CLI tutorial

QDNAseq

             Changes in version 1.33.1 (2022-04-27)                 

MISCELLANEOUS

• Now the package gives an informative error message when an outdated version of the ‘future’ package is used. It requires future (>= 1.22.1).

BUG FIXES

• A few functions used class(x) == “data.frame” rather than inherits(x, “data.frame”).

             Changes in version 1.33.0 (2022-04-26)                 
  

• The version number was bumped for the Bioconductor devel version, which is now BioC 3.16 for R-devel.

QFeatures

                     Changes in version 1.7                         

QFeatures 1.7.3

• fix: fixed filterFeatures when selection contains environment variables

QFeatures 1.7.2

• feat: added ‘c’ methods to combine QFeatures objects.
• feat: added nrows and ncols methods. Also added use.names argument (cf ?BiocGenerics::dims)
• docs: improved docs for filterFeatures()
• tests: improved unit tests for filterFeatures()
• feat: added a keep argument in filterFeatures() to control whether to keep or remove features for assays that do not contain the filter variable. Also added message printing for a better overview of which variable were found.
• fix: fixed addAssay() to solve issue #104.
• refactor: refactored addAssay() and dramatically improved the usage of computational resources.
• feat: colData is automatically transferred from the assay to the QFeatures object.
• feat: implemented removeAssay() and replaceAssay(). Together with addAssay(), these functions are used to implement the replacement method [[<- required to solve issue #57.
• Add CC-BY-SA license for vignettes.

QFeatures 1.7.1

• refactor: imputation now adds a new assay instead of replacing values.

QFeatures 1.7.0

• New Bioc devel version.

qPLEXanalyzer

                   Changes in version 1.15.3                        

• Fix for error in devtools::check tests caused by differing locales

quantiseqr

                    Changes in version 1.6.0                        

Other notes

• Fixed the behavior of the mapGenes function when no duplicate names are found, avoiding unnecessary remapping and having a consistent behavior with the original implementation

RaggedExperiment

                   Changes in version 1.22.0                        

• Add as.list and as.data.frame methods to RaggedExperiment to facilitate extraction of mcols and conversion to table format, respectively.

rawrr

              Changes in version 1.5 (2022-08-22)                   

• Add centroid.PreferredNoises.

Rcpi

             Changes in version 1.33.2 (2022-07-17)                 

Improvements

• Updated the endpoint URL of UniProt API to fix access issues (#14).

             Changes in version 1.33.1 (2022-05-07)                 
  

Improvements

• Remove the Enhances field in DESCRIPTION to improve clarity.

             Changes in version 1.33.0 (2022-04-25)                 
  

Improvements

• Fixed a build error on macOS in the devel branch due to dependencies not available.

RCy3

                   Changes in version 2.18.0                        

• New functions:
  • exportPNG
  • exportJPG
  • exportPDF
  • exportPS
  • exportSVG
  • importFileFromUrl
  • selectEdgesAdjacentToNodes

ReactomePA

                   Changes in version 1.41.1                        

• add function gson_Reactome (2022-7-13, Wed)

reconsi

                    Changes in version 1.9.1                        

• Explicitly load Vandeputte data

rGREAT

                   Changes in version 1.99.7                        

• Calculation has been speeded up.

                   Changes in version 1.99.6                        
  

• set getGeneSetsFromBioMart() public

                   Changes in version 1.99.2                        
  

• by default exclude gap regions

• chr prefix in gr is removed when biomart_dataset is set.

                   Changes in version 1.99.0                        
  

• add great() and related functions to support local GREAT.

• add shinyReport() to export results into a shiny application.

rhdf5

                   Changes in version 2.42.0                        

CHANGES

• Function H5Ocopy() has been included.

• UTF-8 encoded character datsets will be marked as having the same encoding when read into an R session.

BUG FIXES

• h5write() no longer truncates multibyte UTF-8 strings (Thanks to Aaron Lun @LTLA for reporting this and providing a fix, https://github.com/grimbough/rhdf5/issues/111).

Rhdf5lib

                    Changes in version 1.20                         

Bug fixes

• Installation on a system with an existing SZIP library would lead to an empty linking location when linking against the package. This could cause downstream compilation problems on some systems. (thanks to @brgew for reporting and Philippe Bordron @bordron for helpful diagnostics https://github.com/grimbough/rhdf5/issues/109)

• Fixed problem where, on some systems, the AEC library would be installed to a directory named ‘lib64’ rather than ‘lib’ as expected by the package Makevars (thanks to Robby Engelmann @robby81 for reporting this, https://github.com/grimbough/Rhdf5lib/issues/44)

Rhisat2

                   Changes in version 1.13.1                        

• Update hisat2 to v2.2.1

• Include SIMD Everywhere library (https://github.com/simd-everywhere/simde) to support arm64

Rhtslib

                    Changes in version 2.0.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Update htslib to 1.15.1 (was 1.7)

RLSeq

                    Changes in version 1.3.0                        

Bioc 3.16 release with the addition of a noise analysis function.

RMassBank

                    Changes in version 3.7.1                        

• Remove getCompTox() because EPA AcTORWS web services have been retired

• Fix issue #309 when a FileList had no “mode” column

rmelting

                   Changes in version 1.13.3                        

• Revert the Java (>= 11) as SystemRequirements. Removed access to private KeySet in the code.

                   Changes in version 1.13.2                        
  

• Added Java (>= 11) as SystemRequirements.

                   Changes in version 1.13.1                        
  

• Update from MELTING 5.1.1 to MELTING 5.2.0
• Added options for consecutive locked nucleic acids (method.consecutive.locked and method.consecutive.locked.singleMM).

RnBeads

                   Changes in version 2.15.1                        

• Added custom reimplementations of dye-bias and background correction methods from SeSaMe

rols

                    Changes in version 2.25                         

CHANGES IN VERSION 2.25.5

• Fail with useful message when ols query can’t be converted to terms.

CHANGES IN VERSION 2.25.4

• Fix error due to failing term().

CHANGES IN VERSION 2.25.3

• Fix failing unit test since change in GO.

CHANGES IN VERSION 2.25.2

• Fix new error when converting an Ontology to data.frame.

CHANGES IN VERSION 2.25.1

• Fix error when converting term with missing slots to data.frame.

CHANGES IN VERSION 2.25.0

• New devel version (Bioc 3.16)

ropls

                   Changes in version 1.29.32                       

• view: minor modification

                   Changes in version 1.29.30                       
  

• view: minor modification

                   Changes in version 1.29.28                       
  

• view: minor modification

                   Changes in version 1.29.26                       
  

• gg_scoreplot: minor modification

                   Changes in version 1.29.24                       
  

• gg_scoreplot: minor modification

                   Changes in version 1.29.22                       
  

• gg_scoreplot: generic method to be applied either to a SummarizedExperiment or an opls object

                   Changes in version 1.29.20                       
  

• gg_scoreplot: modification of the info to display with plotly

                   Changes in version 1.29.18                       
  

MINOR MODIFICATION

• minor documentation update

                   Changes in version 1.29.16                       
  

MINOR MODIFICATION

• minor documentation update

                   Changes in version 1.29.14                       
  

NEW FEATURE

• NCI60 dataset from omicade4 available in MultiAssayExperiment and MultiDataSet

                   Changes in version 1.29.12                       
  

MINOR MODIFICATION

• minor documentation update

                   Changes in version 1.29.10                       
  

MINOR MODIFICATION

• minor documentation update

                   Changes in version 1.29.8                        
  

NEW FEATURE

• ‘opls’ method now handles MultiAssayExperiment

                   Changes in version 1.29.6                        
  

NEW FEATURE

• ‘opls’ method now handles SummarizedExperiment

                   Changes in version 1.29.4                        
  

NEW FEATURE

• ‘view’ method now handles SummarizedExperiment

• ‘sacurine’ dataset includes the ExpressionSet and SummarizedExperiment formats

                   Changes in version 1.29.2                        
  

MINOR MODIFICATION

• new bioc release

rpx

                     Changes in version 2.5                         

rpx 2.5.1

• Address failing unit test since PRIDE URL has changed back.

rpx 2.5.0

• New bioconductor devel version

rrvgo

                    Changes in version 1.8.1                        

• New features in scatterPlot():
  • dimensionality reduction with UMAP
  • plot only parents

• Fix picking the right point size in scatterPlot()

• Improve vignette

Rsubread

                   Changes in version 2.12.0                        

• Improve the data structure used by cellCounts to further improve its speed.

• More checks for input parameters to prevent cellCounts from crashing.

• Improve the screen output of cellCounts.

RTCGA

                   Changes in version 1.27.2                        

• moved createTCGA() out of the package

                   Changes in version 1.27.1                        
  

• Fixed http and https calls to https://gdac.broadinstitute.org/

RTCGAToolbox

                   Changes in version 2.28.0                        

New features

• Resolve disparate columns in mutation files from GBMLGG (@andreagrioni, #45)
• Update codebase to download https resources from newer layout in gdac.broadinstitute.org (@biostars-nyc, #44).
• Update makeSummarizedExperimentFromGISTIC interface with rownameCol input, type checking, and set row names when the are not duplicated.

Bug fixes and minor improvements

• Use cache directory obtained from tools::R_user_dir
• Clean up class membership checks, e.g., with is(x, “classname”)
• Set missing rows to “” for downstream compatibility with SummarizedExperiment.

S4Vectors

                   Changes in version 0.36.0                        

NEW FEATURES

• Implement DataFrameFactor objects. See ‘?DataFrameFactor’.

• Add droplevels() method for Factor objects.

• Factor objects now use a raw vector instead of an integer vector to store their internal index when they have 255 levels or less. This greatly reduces their memory footprint.

SIGNIFICANT USER-VISIBLE CHANGES

• Subsetting a DataFrame object no longer tries to keep its colnames unique.

sangeranalyseR

                    Changes in version 99.1                         

• Base class: SangerReads is designed to store each forward/revers reads.

                    Changes in version 1.6.1                        
  

• Fix chromatogram color issue.

satuRn

                    Changes in version 1.4.1                        

We report a bug in satuRn 1.4.0. (Bioconductor release 3.15). The bug was inadvertently introduced in satuRn 1.3.1 (from the former Bioconductor devel). Note that the bug was not thus present in any of the older Bioconductor releases 3.13 and 3.14 (satuRn 1.0.x, 1.1.x and 1.2.x).

Bug details:

Imagine a gene with three isoforms and two cell types. The goal is to assess DTU between cell types. All isoforms are expressed in all cells of cell type 1. However, none of the isoforms are expressed in any of the cells in cell type 2 (i.e., the gene is not expressed in cell type 2).

satuRn computes the log-odds of picking a certain isoform from the pool of isoforms in each cell type, and then compares these log-odds estimates between the cell types. However, in this example, the log-odds of picking a certain isoform from the pool of isoforms in cell type 2 cannot be computed, as there is no data. Hence, the DTU test statistic should be NA. However, due to erroneous handling of NA estimates, which was inadvertently introduced in satuRn 1.3.1. while aiming to resolve github issue 16, the log-odds in cell type 1 will be compared to zero. Hence, (erroneous) results can be obtained for this contrast, even when there are no data in cell type 2.

Note that in many cases such isoforms may not pass filtering and would not get evaluated altogether. However, when analyzing sprase scRNA-Seq datasets with a lenient filtering criterium, this problem will apply, and will result in mistakes in the inference.

scater

                   Changes in version 1.26.0                        

• Add projectReducedDim function to project points into an existing reduced dimensionality embedding.

• Support “color” and “colour” spellings in all plotting functions.

• Add order_by argument to cellwise plot functions.

• Add rasterise argument to plotReducedDim using rasterise.

SCFA

             Changes in version 1.7.1 (2022-07-29)                  

• Changed neural network computation from Tensorflow to Torch.

scp

                     Changes in version 1.7                         

scp 1.7.4

• Updated CITATION

scp 1.7.3

• refactor: package complies with BiocCheck
• docs: fixed bug in vignette

scp 1.7.2

• Add CC-BY-SA license for vignettes.

scp 1.7.1

• refactor: removed deprecated function rowDataToDF()
• tests: fixed some tests failing because of SCE version differences.
• feat: users can now specify sep when sample names are automatically generated.

scp 1.7.0

• New devel (Bioc 3.16)

scRepertoire

                    Changes in version 1.7.2                        

• Rebumping the version change with new release of Bioconductor

• Added mean call to the heatmap of vizGenes()

• To combineTCR, filteringMulti now checks to remove list elements with 0 cells.

• Removed top_n() call as it is now deprecated, using slice_max() without ties.

• Add arrange() call during parseTCR() to organize the chains

• Correct the gd flip in the combineContig and subsequent functions

• Removed viridis call in the clonalNetwork() function that was leading to errors

• Matched syntax for strict clonotype in combineBCR()

• Added group.by variable to all applicable visualizations

• Added return.boots to clonalDiversity(), allow for export of all bootstrapped values

scTGIF

                   Changes in version 1.11.1                        

• Some bugs are fixed in reportTGIF()

scuttle

                    Changes in version 1.8.0                        

• Removed support for use.altexps= in aggregateAcrossCells() and logNormCounts().

seqArchR

                    Changes in version 1.1.1                        

• (User-facing) Fixed: Too many warnings from Python’s scikit-learn were being printed to console (warning about an expected change in future scikit-learn version)

SeqArray

                   Changes in version 1.38.0                        

UTILITIES

• new option ‘ext_nbyte’ in seqGet2bGeno()

• seqAlleleCount() and seqGetAF_AC_Missing() return NA instead of zero when all genotypes are missing at a site

• seqGDS2VCF() does not output the FORMAT column if there is no selected sample (e.g., site-only VCF files)

• seqGetData(, "$chrom_pos2") is similar to seqGetData(, "$chrom_pos") except the duplicates with the suffix (“_1”, “_2” or >2)

NEW FEATURES

• seqGDS2BED() can convert to PLINK BED files with the best-guess genotypes when there are only numeric dosages in the GDS file

• seqEmptyFile() outputs an empty GDS file

                   Changes in version 1.36.2                        
  

BUG FIXES

• fix the bug at multi-allelic sites with more than 15 different alleles, see https://github.com/zhengxwen/SeqArray/issues/78

                   Changes in version 1.36.1                        
  

BUG FIXES

• seqExport() failed when there is no variant

• seqSetFilter(, ret.idx=TRUE), see https://github.com/zhengxwen/SeqArray/issues/80

shinyepico

             Changes in version 1.4.2 (2022-05-18)                  

• Bug fixed: dplyr problem with bisulfite plot and contrasts table

             Changes in version 1.4.1 (2022-05-10)                  
  

• Bug fixed: dplyr problem with bisulfite plot and contrasts table

signeR

                    Changes in version 2.0.0                        

• interactive shiny interface: signeRFlow

• Option to work with previously defined signatures, just estimating exposures.

• Parallel processing,

• New method to find the number of signatures (or groups) present in data, based on statistical testes of BIC values,

• Tests of signature association with survival data or continuous variables,

• Exposure-based clustering methods

simplifyEnrichment

                    Changes in version 1.7.2                        

• anno_word_cloud(): fixed a bug where exclude_words is not properly passed to internal functions.

• simplifyGOFromMultipleLists(): fixed a bug where control is not properly passed to internal functions.

• simplifyGOFromMultipleLists(): draw barplots which show numbers of signifiant GO terms in clusters.

singleCellTK

             Changes in version 2.7.3 (2022-10-25)                  

• Fixed bugs related to dependency updates

             Changes in version 2.7.2 (2022-10-19)                  
  

• Deprecated findMarkerDiffExp(), findMarkerTopTable() and plotMarkerDiffExp(), which are replaced by runFindMarker(), getFindMarkerTopTable() and plotFindMarkerHeatmap(), respectively
• Added useReducedDim, detectThresh arguments for find marker functions
• Deprecated getUMAP() and getTSNE(), which are replaced by runUMAP() and runTSNE(), respectively
• Added runQuickUMAP() and runQuickTSNE() functions which directly compute the proper embedding from raw counts matrices with a simplified argument set
• Added arguments aggregateRow and aggregateCol to plotSCEHeatmap()
• Updated output metadata structure of QC functions, as well as combineSCE() which merges the new structure properly
• Refined batch correction function set

• Fixed bugs related to UI and console functions

             Changes in version 2.7.1 (2022-06-29)                  
  

• Refactored scaling related parts of the workflow, including variable feature detection, dimension reduction and 2D embedding
• Redesigned UI landing page and UI running prompt
• Added marker table module across UI
• Added more unit tests
• Fixed bugs in TSCAN UI
• Other minor bug fixes

SingleR

                    Changes in version 2.0.0                        

• The format of the output of trainSingleR() has changed and is no longer back-compatible.

• recompute=FALSE in trainSingleR() does nothing; all integrated analyses are now done with recompute=TRUE. To that end, combineCommonResults() is also deprecated.

• genes = “sd” and its associated options in trainSingleR() are no longer supported.

• first.labels is no longer reported in classifySingleR().

• Added another parallelization mechanism via num.threads= and C++11 threads. This should be much more memory efficient than using BiocParallel.

• combineRecomputedScores() will automatically handle mismatches in the input references by default.

SNPRelate

                   Changes in version 1.32.0                        

• update the web links

                   Changes in version 1.30.1                        
  

• fix a portable issue with Fortran character strings via USE_FC_LEN_T & FCONE

SpatialDecon

             Changes in version 1.8.0 (2022-08-09)                  

• updated package to logNormReg 0.4.0+

• weights were not used in logNormReg 0.3.0, weights are now being used as originally intended

• Bioconductor release 3.16 version

SpatialExperiment

             Changes in version 1.7.2 (2022-10-07)                  

• support for seeing colData names with $ in RStudio

             Changes in version 1.7.1 (2022-07-29)                  
  

• support for reading Space Ranger V2 outputs with read10xVisium()

spatialHeatmap

             Changes in version 2.3.1 (2022-10-22)                  

• In co-visualization, a new feature of bulk-to-cell mapping was developed, co-clustering method was simplified, and Shiny app was updated with options of Annotation/manual, Automatic, cell2bulk, bulk2cell.

• An S4 class of “SVG” was developed to store aSVG instances.

• Vignettes were updated.

Spectra

                     Changes in version 1.7                         

Changes in 1.7.5

• Force serial processing in some unit tests to avoid potential failures on some Bioconductor build and check servers (under some circumstances).

Changes in 1.7.4

• Add MsBackendMemory backend class providing a more efficient in-memory data representation than MsBackendDataFrame.

Changes in 1.7.3

• Import spectrapply from ProtGenerics.

Changes in 1.7.2

• Fix setBackend if provided Spectra is empty.
• backendInitialize,Spectra,MsBackendDataFrame returns a Spectra object with the full provided spectra data.

Changes in 1.7.1

• Add uniqueMsLevels function to allow more efficient, backend-specific, implementations for retrieving unique MS levels from a data set.

splatter

             Changes in version 1.22.0 (2022-10-31)                 

• Fixed a bgg in BASiSSimulate() when spike.means is resampled

• Fixed bugs in splatPopSimulate() with non-matching rownames and when sampling batches

sSNAPPY

             Changes in version 1.1.1 (2022-08-03)                  

• Fixed a missing column name problems in weight_ss_fc

             Changes in version 1.1.0 (2022-06-27)                  
  

• Fixed a few typos

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

SummarizedExperiment

                   Changes in version 1.28.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• SummarizedExperiment objects now accept NAs in their rownames. Important notes:
  • NAs in the rownames are now tolerated but will cause problems downstream e.g. they break the rowData() getter unless ‘use.names=FALSE’ is used.
  • NAs in the colnames are not and cannot be supported at the moment! Right now they break the SummarizedExperiment() constructor in an ugly way (error message not super helpful):

    SummarizedExperiment(m) Error in DataFrame(x = seq_len(ncol(a1)), row.names = nms) : missing values in ‘row.names’ This will need to be improved.

  • At the root of these problems is the fact that at the moment DataFrame objects do NOT support NAs in their rownames. Bottom line: NAs in the dimnames of a SummarizedExperiment object should be avoided at all cost. One way to deal with them is to replace them with empty strings (“”). See commit 71872cc03b7c0195fb80d1d09409243f049ebb3f.
• Small tweak to combineRows/combineCols: combineRows() and combineCols() no longer need to “fix” the dimnames that end up on the combined assays of the returned SummarizedExperiment object. So the assay dimnames are now returned as-is. See commit 1d6610eb168330f32433273e4fe49da173dcd33b.

synapter

                    Changes in version 2.21                         

Changes in version 2.21.1

• Render fragmentmatching.Rmd with rmarkdown::html_document() (see #139)

SynExtend

                   Changes in version 1.9.20                        

• Adds new GeneralizedRF function to calculated information-theoretic Generalized Robinson-Foulds distance between two dendrograms.
• Documentation for new function
• New ProtWeaver predictor based off of GeneralizedRF metric

• New internal C source code for GeneralizedRF

                   Changes in version 1.9.19                        
  

• Adds new DPhyloStatistic function to calculate the D-statistic for a binary state against a phylogeny following Fritz and Purvis (2009).
• Documentation for new function
• new internal C source code for DPhyloStatistic

• new internal C source code for random utility functions, currently only has functions to generate random numbers

                   Changes in version 1.9.18                        
  

• Various internal improvements to presence/absence profile methods

                   Changes in version 1.9.17                        
  

• Adds new prediction algorithm GainLoss
• Adds new internal C implementation of dendrograms, significantly faster than R dendrograms
• ProtWeaver methods Behdenna and GainLoss can now infer a species tree when possible
• Updates Jaccard and Hamming methods to use C implementations for distance calculation
• Adds HammingGL method to calculate Hamming distance of gain/loss events
• Minor bugfixes to ProtWeaver methods relating to subsetting

• Updates to various man pages

                   Changes in version 1.9.16                        
  

• Removes flatdendrapply, function was already included in SynExtend

• minor bugfixes to ProtWeaver

                   Changes in version 1.9.15                        
  

• Edits to SelectByK, function can work as intended, but is still too conservative at false positive removal.

                   Changes in version 1.9.14                        
  

• Adds new function flatdendrapply for more options to apply functions to dendrograms. Function is used in SuperTree.
• Adds new function SuperTree to construct a species tree from a set of gene trees.

• Adds new dataset SuperTreeEx for SuperTree and flatdendrapply examples.

                   Changes in version 1.9.13                        
  

• SelectByK function argument ClusterSelect switched to ClusterScalar. Cluster number selection now performed by fitting sum of total within cluster sum of squares to a right hyperbola and taking the ceiling of the half-max. Scalar allows a user to pick different tolerances to select more, or less clusters. Plotting behavior updated.

                   Changes in version 1.9.12                        
  

• simMat class now supports empty indexing (s[])

• simMat class now supports logical accession (s[c(T,F,T),])

                   Changes in version 1.9.11                        
  

• Added the function SelectByK that allows for quick removal of false positive predicted pairs based on a relatively simple k-means approach. Function is currently designed for use on the single genome-to-genome pairwise comparison, and not on an all-vs-all many genomes scale, though it may provide acceptable results on that scale.

                   Changes in version 1.9.10                        
  

• New simMat class for dist-like similarity matrices that can be manipulated like base matrices
• Major update to ProtWeaver internals
• All internal calls use simMat objects whenever possible to decrease memory footprint
• Note ContextTree and ProfDCA require matrices internally
• ProtWeb objects now inherit from simMat
• ProtWeb.show and ProtWeb.print now display predictions in a more natural way
• GetProtWebData() deprecated; ProtWeb now inherits as.matrix.simMat and as.data.frame.simMat
• New documentation pages for simMat class
• GetProtWebData documentation page reworked into ProtWeb documentation file.

• Fixes new bug in Method=’Hamming’ introduced in SynExtend 1.9.9

                    Changes in version 1.9.9                        
  

• Fixes minor bug in Method=’Hamming’

• Moves some code around

                    Changes in version 1.9.8                        
  

• Major refactor to file structure of ProtWeaver to make individual files more manageable

• Adds new documentation files for individual prediction streams of predict.ProtWeaver

                    Changes in version 1.9.7                        
  

• BlockReconciliation now returns a an object of class PairSummaries.

                    Changes in version 1.9.6                        
  

• Fixes an error where warnings were mistakenly output to the user

                    Changes in version 1.9.5                        
  

• Moves platform-specific files in src/ (originally added by mistake)

                    Changes in version 1.9.4                        
  

• Lots of bugfixes to ResidueMI.ProtWeaver
• predict.ProtWeaver now correctly labels rows/columns with gene names, not numbers
• predict.ProtWeaver now correctly handles Subset arguments

• predict.ProtWeaver(…, Subset=3) will correctly predict for all pairs involving gene 3 (or for any gene x, as long as Subset is a length 1 character or integer vector).

                    Changes in version 1.9.2                        
  

• Adds residue MI method to ProtWeaver
• Various bugfixes for ProtWeaver

systemPipeShiny

                   Changes in version 1.7.03                        

General:

• bump up the version requirement for SPR to 2.2.0, SPRdata to 2.0.0, spsComps to 0.3.2, drawer to 0.2.0.

Minor change:

• Since xl modal is not supported in bs3, change all modal in WF module to l size.
• Fixed some links
• add BiocView keywords to description.

Bug fix:

• As the new version of SPR, when adding a Linewise step R code, if the code is stored inside a variable, this is not supported. However, SPS has to capture user input code as variable. A workaround is used for now to fix this problem, waiting SPR to support a better way of code in variable or quoted code.

TargetDecoy

             Changes in version 1.3.4 (2022-10-21)                  

• limiting the number of dots drawn in the PP-plots (#8, @lievenclement)

• largest decoy score (#8, @lievenclement)

• Vignette: generate Figure 1 from code instead of image file (#8, @lievenclement)

• Update gadget screenshots with new color code (#8, @lievenclement)

             Changes in version 1.3.3 (2022-09-12)                  
  

• Shiny gadget: allow non-numerical variables for Score input

             Changes in version 1.3.2 (2022-06-17)                  
  

• [Fix]: Pass initial argument choices to the gadget
• [Fix]: Made argument name for the log10-transformation consistent (log10)

• evalTargetDecoysHist(): Updated default colors of targets and decoys

             Changes in version 1.3.1 (2022-05-20)                  
  

• Added a NEWS.md file to track changes to the package.
• Added Shiny gadget to interactively select variable names (#7)
• Moved decoyScoreTable() to its own file: R/decoyScoreTable.R

TargetSearch

                    Changes in version 2.0.0                        

NEW FEATURES

• Despite being a 2.0 release, the new features are minimal as this release contains mostly documentation improvements, code refactoring and clean-ups, and bug fixes.

• New methods for combining tsLib, tsRim and tsSample objects. These objects can be combined with the c operator. The method length reports the number of markers for objects of class tsRim.

• The function quantMatrix has been fixed and now it accepts three methods to generate its output. quantmass uses the library’s quantification mass (QM), maxint takes the most abundant mass as QM, and maxobs takes the QM with the most observations. In addition the parameter selmass allows for selection of selective masses only if turned on.

• The function Write.Results has a new parameter selmass that is passed to quantMatrix, and the argument quantMatrix accepts the value quantmass, also passed to quantMatrix. The argument prefix changed its default value from NA to NULL.

BUG FIXES

• C code: use variables of same size (size_t vs int)

• C code: replace and update user-controlled memory interface macros.

• Baseline quantiles. Update quantiles computation with partially sorted data instead of sorted data. This yields a three-fold speed increase.

• Function Profile: set correct rownames. The slots of the msProfile object did not have correct rownames.

• Example data: fix object inconsistencies due to incorrect rownames.

• Plotting functions: they should return invisible().

• Modernize the DESCRIPTION file.

• Import the whole stats package instead of listing each function.

• Replace instances of T/F with TRUE/FALSE in functions and vignettes.

• Add examples to functions that lacked them.

• Fix quantMatrix. The function has been broken for years as it did not work as intended. Nevertheless, the default option quantmass means that the output is now correct (formely, the options maxint and maxobs were simply ignored).

TBSignatureProfiler

                   Changes in version 1.92.0                        

Bug Fixes

• Fixed the tableAUC bootstrapped confidence interval to be the 2.5 and 97.5 percentiles instead of the 5 and 95 percentiles
• Fixed the upper CI value for the pROC/DeLong AUC CI method in the bootstrapAUC function

Major Changes

• Changed tableAUC confidence interval default to bootstrapped instead of DeLong (pROC argument)

Minor Changes

• Updated the github and website introductions.
• Added Natarajan_7, Kaul_3 signatures
• Added Francisco_OD_2, Kwan_186 signatures
• Shortened some example run times

tomoseqr

             Changes in version 1.11.1 (2022-10-25)                 

• Made the following changes: o Added 3D visualize function to imageViewer o Changed normCount and normMask options in estimate3dExpressions() to normalize option. When it is TRUE (default), the function works as if normCount = "count", normMask = TRUE. When it is FALSE, the function works as if normCount = "none", normMask = FALSE.

topdownr

                    Changes in version 1.19                         

Changes in version 1.19.2

• Avoid coercion methods that will be deprecated in Matrix 1.4-2.
• Replace stopifnot calls with if (…) stop calls.

Changes in version 1.19.1

• New version for Bioc 3.17 (devel)
• Rerun latest roxygen2.
• Remove if (getGeneric(…)) statements in AllGenerics.R do avoid problems while reloading the package.

trackViewer

                   Changes in version 1.33.8                        

• Fix a bug if there is no name for the freatures.

                   Changes in version 1.33.7                        
  

• print the more pseudocode in browseTracks.

                   Changes in version 1.33.6                        
  

• Fix the bug for ‘invalid color name’ in browseTracks

• print the pseudocode in browseTracks

                   Changes in version 1.33.5                        
  

• Change the cool file open flag to “H5F_ACC_RDONLY”

                   Changes in version 1.33.4                        
  

• Fix a issue for plot tracks by insert 0 to the first signals.

                   Changes in version 1.33.3                        
  

• Add support for motif logo for lollipop plot.

                   Changes in version 1.33.2                        
  

• Add support for multiple operators for viewTrack.

                   Changes in version 1.33.1                        
  

• Fix the bug when locateScale return NA values.

transomics2cytoscape

                    Changes in version 1.7.1                        

DATA or DOCUMENT CHANGES

• Changed the name of the network layer index in the extdata/usecase1 and 2.

• Changed the Z height value in the extdata/usecase1 and 2.

treeio

                   Changes in version 1.21.3                        

• update as.phylo and as.treedata for data.frame object (2022-10-31, Mon, #88)

• as.phylo() method for list (2022-09-14, Wed, #86)

                   Changes in version 1.21.2                        
  

• update as.treedata.pvclust method (2022-08-15, Mon, #82)

• add citation of the tree data book (2022-08-13, Sat)

                   Changes in version 1.21.1                        
  

• read.nextstrain.json() function to parse json tree file from NextStrain (2022-08-03, Wed, #81)

tximeta

                   Changes in version 1.15.3                        

• Up to GENCODE 42 (H.s.), M31 (M.m), and Ensembl 108

                   Changes in version 1.15.2                        
  

• Up to GENCODE 41 (H.s.), M30 (M.m), and Ensembl 107

tximport

                   Changes in version 1.25.1                        

• Now the ‘eds’ package exports readEDS() instead of ‘fishpond’.

UCell

                    Changes in version 2.1.2                        

• New function SmoothKNN() for k-nearest neighbor smoothing of UCell scores. It can be applied both on SingleCellExperiment and Seurat objects (S3 method).

• Add two new vignettes: along with basic usage (vignette 1), there are now dedicated vignettes for running UCell with SingleCellExperiment objects (vignette 2) and Seurat objects (vignette 3). kNN smoothing is illustrated for both object types.

• Fixing a bug that prevented storing of feature ranks.

UniProt.ws

                   Changes in version 2.38.0                        

USER VISIBLE CHANGES

• UniProt.ws uses the https://rest.uniprot.org/ API interface for queries.
• mapUniprot is an exported function to directly map identifiers via UniProt and is used by the select method.
• allToKeys and allFromKeys provide all the available to and from keys for mapping identifiers
• returnFields provides all the possible inputs to the columns argument in the select and mapUniProt functions (ids in the name column)

Uniquorn

             Changes in version 2.17.3 (2022-10-13)                 

Fixed parsing problem

• Fixd critial install error in R dpendency “Runit””

             Changes in version 2.17.1 (2022-06-28)                 
  

Fixed parsing problem

• minor bugfixes

             Changes in version 2.17.0 (2022-03-22)                 
  

Fixed parsing problem

• Fixed a parsing problem regarding the Cosmic and CCLE. databases

universalmotif

                   Changes in version 1.16.0                        

NEW FEATURES

• write_transfac(name.tag, altname.tag): New arguments to manually set the name and altname tags in the final TRANSFAC motifs.

MINOR CHANGES

• write_matrix(positions): Partial argument matching allowed.

• motif_tree(): Silence messages from ggtree.

BUG FIXES

• create_motif(): Don’t ignore the nsites argument when generating random motifs.

• read_meme(): Correctly parse background if lines are prepended with a space.

• convert_type(pseudocount): Change the pseudocount within the motif when performing a type conversion and the option is set.

                   Changes in version 1.14.1                        
  

BUG FIXES

• read_meme(): Handle motif files with custom alphabets and no ‘END’ line in alphabet definition. Thanks to @manoloff (#24) for the bug report, and Spencer Nystrom for the fix (#25).

updateObject

                    Changes in version 1.2.0                        

• No changes in this version.

variancePartition

                   Changes in version 1.27.6                        

• remove FMT functions

                   Changes in version 1.27.5                        
  

• update dependencies

• make topTable() generic to work with R 4.2.1 and Bioc 3.16

                   Changes in version 1.27.4                        
  

• update dependencies

                   Changes in version 1.27.3                        
  

• update filtering of covariates, especially for when many samples are dropped

                   Changes in version 1.27.1                        
  

• update plotPercentBars arguments

                   Changes in version 1.26.1                        
  

• patch to update docs

vissE

                    Changes in version 1.6.0                        

• Added informative error messages. Improved edge case handling.

wppi

             Changes in version 1.5.1 (2022-06-07)                  

• The workflow calculates Protein-Protein Interaction weights and scores genes
• Database knowledge is automatically fetched from OmniPath, Gene Ontology and Human Phenotype Ontology
• Submitted to Bioconductor

zellkonverter

                    Changes in version 1.8.0                        

Major changes

• Improve compatibility with the R anndata package. This required modifying conversion functions so that Python objects are explicitly converted rather than relying on automatic conversion.

• Added support for numpy recarrays. This solves a long-standing issue and allows results from scanpy’s rank_genes_groups() function to be read.

Minor changes

• The Python version is now pinned in the anndata v0.7.6 environment for compatibility with changes in basilisk

• Instatiate Python environments so they can be properly picked up by basilisk::configureBasiliskEnv()

• Allow missing obs/var names when use_hdf5 = TRUE

• Minor changes to the UI functions for compatibility with cli v3.4.0

• Minor changes for compatibility with Matrix v1.4-2

• Improvements to the UI for warnings

• Updates and improvments to tests

NEWS from existing Data Experiment Packages

curatedMetagenomicData

                    Changes in version 3.6.0                        

• curatedMetagenomicData now contains 22,588 samples from 93 studies

• A total of 2,055 samples added since Bioconductor 3.15 (April 2022)

• Studies added since Bioconductor 3.15 (April 2022):

• BedarfJR_2017 (59 samples)

• IaniroG_2022 (165 samples)

• MetaCardis_2020_a (1,831 samples)

• Both “short” and “NCBI” row names were re-validated against NCBI Taxonomy

depmap

                  Changes in version 1.11.2                        

• 22Q1 data added for crispr, copyNumber, TPM, mutationCalls, metadata and achilles datasets. Note: 22Q2 is the last release to follow a quarterly release schedule. Future Depmap releases will follow a bi-annual release schedule with dataset updates every 6 months.

                  Changes in version 1.11.1                        
  

• EH numbers have been pdated in the latest dataset (see #78)

imcdatasets

             Changes in version 1.5.4 (2022-10-21)                  

• Possibility to retrieve single cell data in the SpatialExperiment format.

             Changes in version 1.5.3 (2022-10-19)                  
  

• Updated all datasets to have consistent object formatting.

• Added dataset versioning.

• Added new dataset loading functions and deprecated the old ones.

• New vignette with guidelines for contribution and dataset formatting.

             Changes in version 1.5.2 (2022-07-04)                  
  

• Updated wrapper functions

• Updated test functions

• Updated BiocViews and documentation

• Added LICENSE file

             Changes in version 1.4.1 (2022-06-29)                  
  

• Added deprecation note for .onLoad functions

NxtIRFdata

             Changes in version 1.3.2 (2022-10-25)                  

• Introducing SpliceWiz for Bioc 3.16 (which replaces NxtIRFcore)

             Changes in version 1.3.1 (2022-10-07)                  
  

• More helpful message when ExperimentHub() fails to load or fails to retrieve Mappability files

RforProteomics

                   Changes in version 1.35.1                        

• Remove failing code chunk.

scpdata

                   Changes in version 1.5.5

• Added package stcker

                   Changes in version 1.5.4  
  

• Fix: fixed character encoding errors

                   Changes in version 1.5.3   
  

• tests: make sure each dataset is available

• docs: don’t run examples. They take too long and crash the checks

                   Changes in version 1.5.2      
  

• Added CITATION

                   Changes in version 1.5.1    
  

• brunner2022: added dataset
• derks2022: added dataset
• add license statements
• leduc2022: added dataset

spatialLIBD

                   Changes in version 1.9.18                        

BUG FIXES

• Fixed a bug related to edgeR::filterByExpr() inside of registration_pseudobulk().

• Moved the min_ncells filtering step to registration_pseudobulk() rather than registration_wrapper() since you should drop low ncells before using edgeR::filterByExpr().

                   Changes in version 1.9.15                        
  

BUG FIXES

• Fixed some bugs in registration_stats_anova() in cases where we only had two different unique values to compute F-statistics with, when we need at least 3.

• Made some parts of registration_stats_anova() and registration_stats_pairwise() more flexible.

• registration_model() now provides a more informative error message when you have an empty factor level, thus leading to a non-full rank model matrix.

                   Changes in version 1.9.12                        
  

NEW FEATURES

• Added functions for computing the modeling statistics used by the spatial registration process. See registration_wrapper() and related functions.

• Added a function for using the output of layer_stat_cor() and for labeling the clusters. This can help interpret the spatial registration results. See annotate_registered_clusters() for more details.

                   Changes in version 1.9.11                        
  

BUG FIXES

• Fixed bugs in gene_set_enrichment() for reverse = TRUE reported by @sparthib.

• Added a reverse option on the shiny app under the gene set enrichment tab, that we tested with the example spe data.

                   Changes in version 1.9.10                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Improved the automatic color palette selector when you switch discrete variables. It also now supports the ManualAnnotation option.

• Discrete variable (cluster) legend is no longer duplicated under the clusters interactive tab.

• You can now search the model test, which helps if you have lots of tests to choose from (this most likely occurs when you are looking at the pairwise results).

                    Changes in version 1.9.9                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Made the shiny application more memory efficient in different areas.

• Changed the default point_size from 1.25 to 2.

• Added the option to show or hide the spatial images on the grid panels in the shiny web application. Turn off by default since it is more efficient.

                    Changes in version 1.9.5                        
  

BUG FIXES

• Fix https://github.com/LieberInstitute/spatialLIBD/issues/41. Reported by @abspangler13. Now the gene selector changes automatically when you change the ‘model results’ (model type) or ‘model test’ inputs. The gene selector is now only shown inside the ‘model boxplots’ panel since it only affects that one.

                    Changes in version 1.9.4                        
  

BUG FIXES

• Fix https://github.com/LieberInstitute/spatialLIBD/issues/40. Reported by @Erik-D-Nelson.

                    Changes in version 1.9.3                        
  

BUG FIXES

• Added a more informative error message when ‘stats’ does not have ENSEMBL gene IDs as the rownames(). Reported by @abspangler13 and @sparthib at https://github.com/LieberInstitute/spatialLIBD/issues/33#issuecomment-1137544893

STexampleData

             Changes in version 1.5.0 (2022-04-27)                  

• reformat datasets to SpatialExperiment version 1.5.3

TargetSearchData

                   Changes in version 1.36.0                        

NEW FEATURES

• Helper functions are added to the package. These functions are a simple interface to retrieve the data files provided by this package. The functions are mostly relevant in TargetSearch examples.

NEWS from existing Workflows

GeoMxWorkflows

                    Changes in version 1.4.0                        

• update links

SingscoreAMLMutations

             Changes in version 1.12.0 (2022-04-05)                 

• Updated data download to download latest version of TCGA data

• Using the matched version (v36) of GENCODE for the data

Deprecated and Defunct Packages

Twenty eight software packages were removed from this release (after being deprecated in Bioc 3.15): ABAEnrichment, Autotuner, BioPlex, CAnD, caOmicsV, clonotypeR, CountClust, diffloop, GCSConnection, GCSFilesystem, GenoGAM, genphen, gprege, networkBMA, Onassis, perturbatr, ppiStats, ProteomicsAnnotationHubData, PSICQUIC, PubScore, Rgin, RmiR, RpsiXML, ScISI, SLGI, Sushi, tofsims, TSRchitect

Please note: phemd and CHETAH, previously announced as deprecated in 3.15, have been updated and remain in Bioconductor.

Thirty software packages are deprecated in this release and will be removed in Bioc 3.17: AffyCompatible, BAC, BitSeq, BrainSABER, bridge, cellTree, coexnet, conclus, ctgGEM, CytoTree, DEComplexDisease, flowCL, flowUtils, gaia, gpart, inveRsion, IsoGeneGUI, iteremoval, MACPET, PoTRA, rama, Rcade, RNASeqR, scAlign, scMAGeCK, sojourner, TCGAbiolinksGUI, TDARACNE, TimeSeriesExperiment, TraRe, tspair, XCIR

Three experimental data packages were removed from this release (after being deprecated in BioC 3.15): DREAM4, MSstatsBioData, ppiData

Two experimental data packages are deprecated in this release and will be removed in Bioc 3.17: gatingMLData, RNASeqRData

Seven annotation packages were removed from this release (after being deprecated in Bioc 3.15): MafH5.gnomAD.v3.1.1.GRCh38_3.13.1.tar.gz, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, SNPlocs.Hsapiens.dbSNP151.GRCh38, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38

No annotation packages were deprecated in this release and will be removed in Bioc 3.17.

One workflow package was removed from this release (after being deprecated in Bioc 3.15) proteomics

No workflow packages were deprecated in this release and will be removed in 3.17.