April 27, 2022

Bioconductors:

We are pleased to announce Bioconductor 3.15, consisting of 2140 software packages, 410 experiment data packages, 909 annotation packages, 29 workflows and 8 books.

There are 78 new software packages, 5 new data experiment packages, 8 new annotation packages, no new workflows, no new books, and many updates and improvements to existing packages.

Bioconductor 3.15 is compatible with R 4.2.0, and is supported on Linux, 64-bit Windows, and Intel 64-bit macOS 10.13 (High Sierra) or higher. We do not currently support arm64 so arm64 Mac users who wish to install Bioconductor Mac binary packages must install the Intel 64-bit build of R available on CRAN. This release will 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 3.15
• New Software Packages
• New Data Experiment Packages
• New Annotation Packages
• New Workflow
• New Books
• NEWS from new and existing software packages
• NEWS from new and existing data experiment packages
• NEWS from new and existing workflows
• Deprecated and Defunct Packages

Getting Started with Bioconductor 3.15

To update to or install Bioconductor 3.15:

1. Install R 4.2.0. Bioconductor 3.15 has been designed expressly for this version of R.

2. Follow the instructions at Installing Bioconductor.

New Software Packages

There are 78 new software packages in this release of Bioconductor.

• APL APL is a package developed for computation of Association Plots (AP), a method for visualization and analysis of single cell transcriptomics data. The main focus of APL is the identification of genes characteristic for individual clusters of cells from input data. The package performs correspondence analysis (CA) and allows to identify cluster-specific genes using Association Plots. Additionally, APL computes the cluster-specificity scores for all genes which allows to rank the genes by their specificity for a selected cell cluster of interest.

• ASURAT ASURAT is a software for single-cell data analysis. Using ASURAT, one can simultaneously perform unsupervised clustering and biological interpretation in terms of cell type, disease, biological process, and signaling pathway activity. Inputting a single-cell RNA-seq data and knowledge-based databases, such as Cell Ontology, Gene Ontology, KEGG, etc., ASURAT transforms gene expression tables into original multivariate tables, termed sign-by-sample matrices (SSMs).

• bandle The Bandle package enables the analysis and visualisation of differential localisation experiments using mass-spectrometry data. Experimental method supported include dynamic LOPIT-DC, hyperLOPIT, Dynamic Organellar Maps, Dynamic PCP. It provides Bioconductor infrastructure to analyse these data.

• beer BEER implements a Bayesian model for analyzing phage-immunoprecipitation sequencing (PhIP-seq) data. Given a PhIPData object, BEER returns posterior probabilities of enriched antibody responses, point estimates for the relative fold-change in comparison to negative control samples, and more. Additionally, BEER provides a convenient implementation for using edgeR to identify enriched antibody responses.

• biodbExpasy The biodbExpasy library provides access to Expasy ENZYME database, using biodb package framework. It allows to retrieve entries by their accession number. Web services can be accessed for searching the database by name or comments.

• biodbMirbase The biodbMirbase library is an extension of the biodb framework package, that provides access to miRBase mature database. It allows to retrieve entries by their accession number, and run specific web services. Description: The biodbMirbase library provides access to the miRBase Database, using biodb package framework.

• biodbNcbi The biodbNcbi library provides access to the NCBI databases CCDS, Gene, Pubchem Comp and Pubchem Subst, using biodb package framework. It allows to retrieve entries by their accession number. Web services can be accessed for searching the database by name or mass.

• biodbNci The biodbNci library is an extension of the biodb framework package. It provides access to biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database. It allows to retrieve entries by their accession number, and run specific web services.

• BOBaFIT This package provides a method to refit and correct the diploid region in copy number profiles. It uses a clustering algorithm to identify pathology-specific normal (diploid) chromosomes and then use their copy number signal to refit the whole profile. The package is composed by three functions: DRrefit (the main function), ComputeNormalChromosome and PlotCluster.

• borealis Borealis is an R library performing outlier analysis for count-based bisulfite sequencing data. It detectes outlier methylated CpG sites from bisulfite sequencing (BS-seq). The core of Borealis is modeling Beta-Binomial distributions. This can be useful for rare disease diagnoses.

• CBEA This package implements CBEA, a method to perform set-based analysis for microbiome relative abundance data. This approach constructs a competitive balance between taxa within the set and remainder taxa per sample. More details can be found in the Nguyen et al. 2021+ manuscript. Additionally, this package adds support functions to help users perform taxa-set enrichment analyses using existing gene set analysis methods. In the future we hope to also provide curated knowledge driven taxa sets.

• cellxgenedp The cellxgene data portal (https://cellxgene.cziscience.com/) provides a graphical user interface to collections of single-cell sequence data processed in standard ways to ‘count matrix’ summaries. The cellxgenedp package provides an alternative, R-based inteface, allowind data discovery, viewing, and downloading.

• CNVMetrics The CNVMetrics package calculates similarity metrics to facilitate copy number variant comparison among samples and/or methods. Similarity metrics can be employed to compare CNV profiles of genetically unrelated samples as well as those with a common genetic background. Some metrics are based on the shared amplified/deleted regions while other metrics rely on the level of amplification/deletion. The data type used as input is a plain text file containing the genomic position of the copy number variations, as well as the status and/or the log2 ratio values. Finally, a visualization tool is provided to explore resulting metrics.

• cogeqc cogeqc aims to facilitate systematic quality checks on standard comparative genomics analyses to help researchers detect issues and select the most suitable parameters for each data set. cogeqc can be used to asses: i. genome assembly quality with BUSCOs; ii. orthogroup inference using a protein domain-based approach and; iii. synteny detection using synteny network properties. There are also data visualization functions to explore QC summary statistics.

• comapr comapr detects crossover intervals for single gametes from their haplotype states sequences and stores the crossovers in GRanges object. The genetic distances can then be calculated via the mapping functions using estimated crossover rates for maker intervals. Visualisation functions for plotting interval-based genetic map or cumulative genetic distances are implemented, which help reveal the variation of crossovers landscapes across the genome and across individuals.

• coMethDMR coMethDMR identifies genomic regions associated with continuous phenotypes by optimally leverages covariations among CpGs within predefined genomic regions. Instead of testing all CpGs within a genomic region, coMethDMR carries out an additional step that selects co-methylated sub-regions first without using any outcome information. Next, coMethDMR tests association between methylation within the sub-region and continuous phenotype using a random coefficient mixed effects model, which models both variations between CpG sites within the region and differential methylation simultaneously.

• CompoundDb CompoundDb provides functionality to create and use (chemical) compound annotation databases from a variety of different sources such as LipidMaps, HMDB, ChEBI or MassBank. The database format allows to store in addition MS/MS spectra along with compound information. The package provides also a backend for Bioconductor’s Spectra package and allows thus to match experimetal MS/MS spectra against MS/MS spectra in the database. Databases can be stored in SQLite format and are thus portable.

• COTAN Statistical and computational method to analyze the co-expression of gene pairs at single cell level. It provides the foundation for single-cell gene interactome analysis. The basic idea is studying the zero UMI counts’ distribution instead of focusing on positive counts; this is done with a generalized contingency tables framework. COTAN can effectively assess the correlated or anti-correlated expression of gene pairs. It provides a numerical index related to the correlation and an approximate p-value for the associated independence test. COTAN can also evaluate whether single genes are differentially expressed, scoring them with a newly defined global differentiation index. Moreover, this approach provides ways to plot and cluster genes according to their co-expression pattern with other genes, effectively helping the study of gene interactions and becoming a new tool to identify cell-identity marker genes.

• crisprBase Provides S4 classes for general nucleases, CRISPR nucleases and base editors. Several CRISPR-specific genome arithmetic functions are implemented to help extract genomic coordinates of spacer and protospacer sequences. Commonly-used CRISPR nuclease objects are provided that can be readily used in other packages. Both DNA- and RNA-targeting nucleases are supported.

• crisprBowtie Provides a user-friendly interface to map on-targets and off-targets of CRISPR gRNA spacer sequences using bowtie. The alignment is fast, and can be performed using either commonly-used or custom CRISPR nucleases. The alignment can work with any reference or custom genomes. Both DNA- and RNA-targeting nucleases are supported.

• crisprBwa Provides a user-friendly interface to map on-targets and off-targets of CRISPR gRNA spacer sequences using bwa. The alignment is fast, and can be performed using either commonly-used or custom CRISPR nucleases. The alignment can work with any reference or custom genomes. Currently not supported on Windows machines.

• crisprScore Provides R wrappers of several on-target and off-target scoring methods for CRISPR guide RNAs (gRNAs). The following nucleases are supported: SpCas9, AsCas12a, enAsCas12a, and RfxCas13d (CasRx). The available on-target cutting efficiency scoring methods are RuleSet1, Azimuth, DeepHF, DeepCpf1, enPAM+GB, and CRISPRscan. Both the CFD and MIT scoring methods are available for off-target specificity prediction. The package also provides a Lindel-derived score to predict the probability of a gRNA to produce indels inducing a frameshift for the Cas9 nuclease. Note that DeepHF, DeepCpf1 and enPAM+GB are not available on Windows machines.

• cytoMEM MEM, Marker Enrichment Modeling, automatically generates and displays quantitative labels for cell populations that have been identified from single-cell data. The input for MEM is a dataset that has pre-clustered or pre-gated populations with cells in rows and features in columns. Labels convey a list of measured features and the features’ levels of relative enrichment on each population. MEM can be applied to a wide variety of data types and can compare between MEM labels from flow cytometry, mass cytometry, single cell RNA-seq, and spectral flow cytometry using RMSD.

• DepInfeR DepInfeR integrates two experimentally accessible input data matrices: the drug sensitivity profiles of cancer cell lines or primary tumors ex-vivo (X), and the drug affinities of a set of proteins (Y), to infer a matrix of molecular protein dependencies of the cancers (ß). DepInfeR deconvolutes the protein inhibition effect on the viability phenotype by using regularized multivariate linear regression. It assigns a “dependence coefficient” to each protein and each sample, and therefore could be used to gain a causal and accurate understanding of functional consequences of genomic aberrations in a heterogeneous disease, as well as to guide the choice of pharmacological intervention for a specific cancer type, sub-type, or an individual patient. For more information, please read out preprint on bioRxiv: https://doi.org/10.1101/2022.01.11.475864.

• DifferentialRegulation DifferentialRegulation is a method for detecting differentially regulated genes between two groups of samples (e.g., healthy vs. disease, or treated vs. untreated samples), by targeting differences in the balance of spliced and unspliced mRNA abundances, obtained from single-cell RNA-sequencing (scRNA-seq) data. DifferentialRegulation accounts for the sample-to-sample variability, and embeds multiple samples in a Bayesian hierarchical model. In particular, when reads are compatible with multiple genes or multiple splicing versions of a gene (unspliced spliced or ambiguous), the method allocates these multi-mapping reads to the gene of origin and their splicing version. Parameters are inferred via Markov chain Monte Carlo (MCMC) techniques (Metropolis-within-Gibbs).

• EpiCompare EpiCompare is used to compare and analyse epigenetic datasets for quality control and benchmarking purposes. The package outputs an HTML report consisting of three sections: (1. General metrics) Metrics on peaks (percentage of blacklisted and non-standard peaks, and peak widths) and fragments (duplication rate) of samples, (2. Peak overlap) Percentage and statistical significance of overlapping and non-overlapping peaks. Also includes upset plot and (3. Functional annotation) functional annotation (ChromHMM, ChIPseeker and enrichment analysis) of peaks. Also includes peak enrichment around TSS.

• epimutacions The package includes some statistical outlier detection methods for epimutations detection in DNA methylation data. The methods included in the package are MANOVA, Multivariate linear models, isolation forest, robust mahalanobis distance, quantile and beta. The methods compare a case sample with a suspected disease against a reference panel (composed of healthy individuals) to identify epimutations in the given case sample. It also contains functions to annotate and visualize the identified epimutations.

• extraChIPs This package builds on existing tools and adds some simple but extremely useful capabilities for working with ChIP-Seq data. The focus is on detecting differential binding windows/regions. One set of functions focusses on set-operations retaining mcols for GRanges objects, whilst another group of functions are to aid visualisatino of results. Coercion to tibble objects is also included.

• fastreeR Calculate distances, build phylogenetic trees or perform hierarchical clustering between the samples of a VCF or FASTA file. Functions are implemented in Java and called via rJava. Parallel implementation that operates directly on the VCF or FASTA file for fast execution.

• GBScleanR GBScleanR is a package for quality check, filtering, and error correction of genotype data derived from next generation sequcener (NGS) based genotyping platforms. GBScleanR takes Variant Call Format (VCF) file as input. The main function of this package is estGeno() which estimates the true genotypes of samples from given read counts for genotype markers using a hidden Markov model with incorporating uneven observation ratio of allelic reads. This implementation gives robust genotype estimation even in noisy genotype data usually observed in Genotyping-By-Sequnencing (GBS) and similar methods, e.g. RADseq. The current implementation accepts genotype data of a diploid population at any generation of multi-parental cross, e.g. biparental F2 from inbred parents, biparental F2 from outbred parents, and 8-way recombinant inbred lines (8-way RILs) which can be refered to as MAGIC population.

• GenomicInteractionNodes The GenomicInteractionNodes package can import interactions from bedpe file and define the interaction nodes, the genomic interaction sites with multiple interaction loops. The interaction nodes is a binding platform regulates one or multiple genes. The detected interaction nodes will be annotated for downstream validation.

• GenProSeq Generative modeling for protein engineering is key to solving fundamental problems in synthetic biology, medicine, and material science. Machine learning has enabled us to generate useful protein sequences on a variety of scales. Generative models are machine learning methods which seek to model the distribution underlying the data, allowing for the generation of novel samples with similar properties to those on which the model was trained. Generative models of proteins can learn biologically meaningful representations helpful for a variety of downstream tasks. Furthermore, they can learn to generate protein sequences that have not been observed before and to assign higher probability to protein sequences that satisfy desired criteria. In this package, common deep generative models for protein sequences, such as variational autoencoder (VAE), generative adversarial networks (GAN), and autoregressive models are available. In the VAE and GAN, the Word2vec is used for embedding. The transformer encoder is applied to protein sequences for the autoregressive model.

• ggmanh Manhattan plot and QQ Plot are commonly used to visualize the end result of Genome Wide Association Study. The “ggmanh” package aims to keep the generation of these plots simple while maintaining customizability. Main functions include manhattan_plot, qqunif, and thinPoints.

• GRaNIE Genetic variants associated with diseases often affect non-coding regions, thus likely having a regulatory role. To understand the effects of genetic variants in these regulatory regions, identifying genes that are modulated by specific regulatory elements (REs) is crucial. The effect of gene regulatory elements, such as enhancers, is often cell-type specific, likely because the combinations of transcription factors (TFs) that are regulating a given enhancer have celltype specific activity. This TF activity can be quantified with existing tools such as diffTF and captures differences in binding of a TF in open chromatin regions. Collectively, this forms a gene regulatory network (GRN) with cell-type and data-specific TF-RE and RE-gene links. Here, we reconstruct such a GRN using bulk RNAseq and open chromatin (e.g., using ATACseq or ChIPseq for open chromatin marks) and optionally TF activity data. Our network contains different types of links, connecting TFs to regulatory elements, the latter of which is connected to genes in the vicinity or within the same chromatin domain (TAD). We use a statistical framework to assign empirical FDRs and weights to all links using a permutation-based approach.

• hermes Provides classes and functions for quality control, filtering, normalization and differential expression analysis of pre-processed RNA-seq data. Data can be imported from SummarizedExperiment as well as matrix objects and can be annotated from BioMart. Filtering for genes without too low expression or containing required annotations, as well as filtering for samples with sufficient correlation to other samples or total number of reads is supported. The standard normalization methods including cpm, rpkm and tpm can be used, and DESeq2 as well as voom differential expression analyses are available.

• lineagespot Lineagespot is a framework written in R, and aims to identify SARS-CoV-2 related mutations based on a single (or a list) of variant(s) file(s) (i.e., variant calling format). The method can facilitate the detection of SARS-CoV-2 lineages in wastewater samples using next generation sequencing, and attempts to infer the potential distribution of the SARS-CoV-2 lineages.

• LinTInd When we combine gene-editing technology and sequencing technology, we need to reconstruct a lineage tree from alleles generated and calculate the similarity between each pair of groups. FindIndel() and IndelForm() function will help you align each read to reference sequence and generate scar form strings respectively. IndelIdents() function will help you to define a scar form for each cell or read. IndelPlot() function will help you to visualize the distribution of deletion and insertion. TagProcess() function will help you to extract indels for each cell or read. TagDist() function will help you to calculate the similarity between each pair of groups across the indwells they contain. BuildTree() function will help you to reconstruct a tree. PlotTree() function will help you to visualize the tree.

• Macarron Macarron is a workflow for the prioritization of potentially bioactive metabolites from metabolomics experiments. Prioritization integrates strengths of evidences of bioactivity such as covariation with a known metabolite, abundance relative to a known metabolite and association with an environmental or phenotypic indicator of bioactivity. Broadly, the workflow consists of stratified clustering of metabolic spectral features which co-vary in abundance in a condition, transfer of functional annotations, estimation of relative abundance and differential abundance analysis to identify associations between features and phenotype/condition.

• MBECS The Microbiome Batch Effect Correction Suite (MBECS) provides a set of functions to evaluate and mitigate unwated noise due to processing in batches. To that end it incorporates a host of batch correcting algorithms (BECA) from various packages. In addition it offers a correction and reporting pipeline that provides a preliminary look at the characteristics of a data-set before and after correcting for batch effects.

• mbOmic The mbOmic package contains a set of analysis functions for microbiomics and metabolomics data, designed to analyze the inter-omic correlation between microbiology and metabolites. Integrative analysis of the microbiome and metabolome is the aim of mbOmic. Additionally, the identification of enterotype using the gut microbiota abundance is preliminaryimplemented.

• MetaboAnnotation High level functions to assist in annotation of (metabolomics) data sets. These include functions to perform simple tentative annotations based on mass matching but also functions to consider m/z and retention times for annotation of LC-MS features given that respective reference values are available. In addition, the function provides high-level functions to simplify matching of LC-MS/MS spectra against spectral libraries and objects and functionality to represent and manage such matched data.

• MobilityTransformR MobilityTransformR collects a tool set for effective mobility scale transformation of CE-MS/MS data in order to increase reproducibility. It provides functionality to determine the migration times from mobility markers that have been added to the analysis and performs the transformation based on these markers. MobilityTransformR supports the conversion of numeric vectors, Spectra-objects, and MSnOnDiskExp.

• Motif2Site Detect binding sites using motifs IUPAC sequence or bed coordinates and ChIP-seq experiments in bed or bam format. Combine/compare binding sites across experiments, tissues, or conditions. All normalization and differential steps are done using TMM-GLM method. Signal decomposition is done by setting motifs as the centers of the mixture of normal distribution curves.

• MSA2dist MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis. It uses scoring matrices to be used in these pairwise distance calcualtions which can be adapted to any scoring for DNA or AA characters. E.g. by using literal distances MSA2dist calcualtes pairwise IUPAC distances.

• MsBackendMsp Mass spectrometry (MS) data backend supporting import and handling of MS/MS spectra from NIST MSP Format (msp) files. Import of data from files with different MSP flavours is supported. Objects from this package add support for MSP files to Bioconductor’s Spectra package. This package is thus not supposed to be used without the Spectra package that provides a complete infrastructure for MS data handling.

• MuData Save MultiAssayExperiments to h5mu files supported by muon and mudata. Muon is a Python framework for multimodal omics data analysis. It uses an HDF5-based format for data storage.

• netZooR PANDA(Passing Attributes between Networks for Data Assimilation) is a message-passing model to reconstruction gene regulatory network. It integrates multiple sources of biological data, including protein-protein interaction data, gene expression data, and sequence motif information to reconstruct genome-wide, condition-specific regulatory networks.[(Glass et al. 2013)]. LIONESS(Linear Interpolation to Obtain Network Estimates for Single Samples) is a method to estimate sample-specific regulatory networks by applying linear interpolation to the predictions made by existing aggregate network inference approaches. CONDOR(COmplex Network Description Of Regulators)is a bipartite community structure analysis tool of biological networks, especially eQTL networks, including a method for scoring nodes based on their modularity contribution.[(Platig et al. 2016). ALPACA(ALtered Partitions Across Community Architectures) is a method for comparing two genome-scale networks derived from different phenotypic states to identify condition-specific modules. [(Padi and Quackenbush 2018)]. This package integrates pypanda–the Python implementation of PANDA and LIONESS(https://github.com/davidvi/pypanda),the R implementation of CONDOR(https://github.com/jplatig/condor) and the R implementation of ALPACA (https://github.com/meghapadi/ALPACA) into one workflow. Each tool can be call in this package by one function, and the relevant output could be accessible in current R session for downstream analysis.

• nnSVG Method for scalable identification of spatially variable genes (SVGs) in spatially-resolved transcriptomics data. The method is based on nearest-neighbor Gaussian processes and uses the BRISC algorithm for model fitting and parameter estimation. Allows identification and ranking of SVGs with flexible length scales across a tissue slide or within spatial domains defined by covariates. Scales linearly with the number of spatial locations and can be applied to datasets containing thousands or more spatial locations.

• OGRE OGRE calculates overlap between user defined genomic region datasets. Any regions can be supplied i.e. genes, SNPs, or reads from sequencing experiments. Key numbers help analyse the extend of overlaps which can also be visualized at a genomic level.

• omicsViewer omicsViewer visualizes ExpressionSet (or SummarizedExperiment) in an interactive way. The omicsViewer has a separate back- and front-end. In the back-end, users need to prepare an ExpressionSet that contains all the necessary information for the downstream data interpretation. Some extra requirements on the headers of phenotype data or feature data are imposed so that the provided information can be clearly recognized by the front-end, at the same time, keep a minimum modification on the existing ExpressionSet object. The pure dependency on R/Bioconductor guarantees maximum flexibility in the statistical analysis in the back-end. Once the ExpressionSet is prepared, it can be visualized using the front-end, implemented by shiny and plotly. Both features and samples could be selected from (data) tables or graphs (scatter plot/heatmap). Different types of analyses, such as enrichment analysis (using Bioconductor package fgsea or fisher’s exact test) and STRING network analysis, will be performed on the fly and the results are visualized simultaneously. When a subset of samples and a phenotype variable is selected, a significance test on means (t-test or ranked based test; when phenotype variable is quantitative) or test of independence (chi-square or fisher’s exact test; when phenotype data is categorical) will be performed to test the association between the phenotype of interest with the selected samples. Additionally, other analyses can be easily added as extra shiny modules. Therefore, omicsViewer will greatly facilitate data exploration, many different hypotheses can be explored in a short time without the need for knowledge of R. In addition, the resulting data could be easily shared using a shiny server. Otherwise, a standalone version of omicsViewer together with designated omics data could be easily created by integrating it with portable R, which can be shared with collaborators or submitted as supplementary data together with a manuscript.

• ompBAM This packages provides C++ header files for developers wishing to create R packages that processes BAM files. ompBAM automates file access, memory management, and handling of multiple threads ‘behind the scenes’, so developers can focus on creating domain-specific functionality. The included vignette contains detailed documentation of this API, including quick-start instructions to create a new ompBAM-based package, and step-by-step explanation of the functionality behind the example packaged included within ompBAM.

• PanomiR PanomiR is a package to detect miRNAs that target groups of pathways from gene expression data. This package provides functionality for generating pathway activity profiles, determining differentially activated pathways between user-specified conditions, determining clusters of pathways via the PCxN package, and generating miRNAs targeting clusters of pathways. These function can be used separately or sequentially to analyze RNA-Seq data.

• pareg Compute pathway enrichment scores while accounting for term-term relations. This package uses a regularized multiple linear regression to regress differential expression p-values obtained from multi-condition experiments on a pathway membership matrix. By doing so, it is able to incorporate additional biological knowledge into the enrichment analysis and to estimate pathway enrichment scores more robustly.

• protGear A generic three-step pre-processing package for protein microarray data. This package contains different data pre-processing procedures to allow comparison of their performance.These steps are background correction, the coefficient of variation (CV) based filtering, batch correction and normalization.

• PSMatch The PSMatch package helps proteomics practitioners to load, handle and manage Peptide Spectrum Matches. It provides functions to model peptide-protein relations as adjacency matrices and connected components, visualise these as graphs and make informed decision about shared peptide filtering. The package also provides functions to calculate and visualise MS2 fragment ions.

• qmtools The qmtools (quantitative metabolomics tools) package provides basic tools for processing quantitative metabolomics data with the standard SummarizedExperiment class. This includes functions for imputation, normalization, feature filtering, feature clustering, dimension-reduction, and visualization to help users prepare data for statistical analysis. Several functions in this package could also be used in other types of omics data.

• qsvaR The qsvaR package contains functions for removing the effect of degration in rna-seq data from postmortem brain tissue. The package is equipped to help users generate principal components associated with degradation. The components can be used in differential expression analysis to remove the effects of degradation.

• RAREsim Haplotype simulations of rare variant genetic data that emulates real data can be performed with RAREsim. RAREsim uses the expected number of variants in MAC bins - either as provided by default parameters or estimated from target data - and an abundance of rare variants as simulated HAPGEN2 to probabilistically prune variants. RAREsim produces haplotypes that emulate real sequencing data with respect to the total number of variants, allele frequency spectrum, haplotype structure, and variant annotation.

• Rbwa Provides an R wrapper for BWA alignment algorithms. Both BWA-backtrack and BWA-MEM are available. Convenience function to build a BWA index from a reference genome is also provided. Currently not supported for Windows machines.

• RCX Create, handle, validate, visualize and convert networks in the Cytoscape exchange (CX) format to standard data types and objects. The package also provides conversion to and from objects of iGraph and graphNEL. The CX format is also used by the NDEx platform, a online commons for biological networks, and the network visualization software Cytocape.

• rgoslin The R implementation for the Grammar of Succint Lipid Nomenclature parses different short hand notation dialects for lipid names. It normalizes them to a standard name. It further provides calculated monoisotopic masses and sum formulas for each successfully parsed lipid name and supplements it with LIPID MAPS Category and Class information. Also, the structural level and further structural details about the head group, fatty acyls and functional groups are returned, where applicable.

• rifi ‘rifi’ analyses data from rifampicin time series created by microarray or RNAseq. ‘rifi’ is a transcriptome data analysis tool for the holistic identification of transcription and decay associated processes. The decay constants and the delay of the onset of decay is fitted for each probe/bin. Subsequently, probes/bins of equal properties are combined into segments by dynamic programming, independent of a existing genome annotation. This allows to detect transcript segments of different stability or transcriptional events within one annotated gene. In addition to the classic decay constant/half-life analysis, ‘rifi’ detects processing sites, transcription pausing sites, internal transcription start sites in operons, sites of partial transcription termination in operons, identifies areas of likely transcriptional interference by the collision mechanism and gives an estimate of the transcription velocity. All data are integrated to give an estimate of continous transcriptional units, i.e. operons. Comprehensive output tables and visualizations of the full genome result and the individual fits for all probes/bins are produced.

• RolDE RolDE detects longitudinal differential expression between two conditions in noisy high-troughput data. Suitable even for data with a moderate amount of missing values.RolDE is a composite method, consisting of three independent modules with different approaches to detecting longitudinal differential expression. The combination of these diverse modules allows RolDE to robustly detect varying differences in longitudinal trends and expression levels in diverse data types and experimental settings.

• rprimer Functions, workflow, and a Shiny application for visualizing sequence conservation and designing degenerate primers, probes, and (RT)-(q/d)PCR assays from a multiple DNA sequence alignment. The results can be presented in data frame format and visualized as dashboard-like plots. For more information, please see the package vignette.

• sccomp A robust and outlier-aware method for testing differential tissue composition from single-cell data. This model can infer changes in tissue composition and heterogeneity, and can produce realistic data simulations based on any existing dataset. This model can also transfer knowledge from a large set of integrated datasets to increase accuracy further.

• seqArchR seqArchR enables unsupervised discovery of de novo clusters with characteristic sequence architectures characterized by position-specific motifs or composition of stretches of nucleotides, e.g., CG-richness. seqArchR does not require any specifications w.r.t. the number of clusters, the length of any individual motifs, or the distance between motifs if and when they occur in pairs/groups; it directly detects them from the data. seqArchR uses non-negative matrix factorization (NMF) as its backbone, and employs a chunking-based iterative procedure that enables processing of large sequence collections efficiently. Wrapper functions are provided for visualizing cluster architectures as sequence logos.

• single Accurate consensus sequence from nanopore reads of a DNA gene library. SINGLe corrects for systematic errors in nanopore sequencing reads of gene libraries and it retrieves true consensus sequences of variants identified by a barcode, needing only a few reads per variant. More information in preprint doi: https://doi.org/10.1101/2020.03.25.007146.

• SPOTlight SPOTlightprovides a method to deconvolute spatial transcriptomics spots using a seeded NMF approach along with visualization tools to assess the results. Spatially resolved gene expression profiles are key to understand tissue organization and function. However, novel spatial transcriptomics (ST) profiling techniques lack single-cell resolution and require a combination with single-cell RNA sequencing (scRNA-seq) information to deconvolute the spatially indexed datasets. Leveraging the strengths of both data types, we developed SPOTlight, a computational tool that enables the integration of ST with scRNA-seq data to infer the location of cell types and states within a complex tissue. SPOTlight is centered around a seeded non-negative matrix factorization (NMF) regression, initialized using cell-type marker genes and non-negative least squares (NNLS) to subsequently deconvolute ST capture locations (spots).

• sSNAPPY A single sample pathway pertrubation testing methods for RNA-seq data. The method propagate changes in gene expression down gene-set topologies to compute single-sample directional pathway perturbation scores that reflect potentail directions of changes.Perturbation scores can be used to test significance of pathway perturbation at both individual-sample and treatment levels.

• standR standR is an user-friendly R package providing functions to assist conducting good-practice analysis of Nanostring’s GeoMX DSP data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. standR allows data inspection, quality control, normalization, batch correction and evaluation with informative visualizations.

• STdeconvolve STdeconvolve as an unsupervised, reference-free approach to infer latent cell-type proportions and transcriptional profiles within multi-cellular spatially-resolved pixels from spatial transcriptomics (ST) datasets. STdeconvolve builds on latent Dirichlet allocation (LDA), a generative statistical model commonly used in natural language processing for discovering latent topics in collections of documents. In the context of natural language processing, given a count matrix of words in documents, LDA infers the distribution of words for each topic and the distribution of topics in each document. In the context of ST data, given a count matrix of gene expression in multi-cellular ST pixels, STdeconvolve applies LDA to infer the putative transcriptional profile for each cell-type and the proportional representation of each cell-type in each multi-cellular ST pixel.

• TEKRABber TEKRABber is made to provide a user-friendly pipeline for comparing orthologs and transposable elements (TEs) between two species. It considers the orthology confidence between two species from BioMart to normalize expression counts and detect differentially expressed orthologs/TEs. Then it provides one to one correlation analysis for desired orthologs and TEs. There is also an app function to have a first insight on the result. Users can prepare orthologs/TEs RNA-seq expression data by their own preference to run TEKRABber following the data structure mentioned in the vignettes.

• terraTCGAdata Leverage the existing open access TCGA data on Terra with well-established Bioconductor infrastructure. Make use of the Terra data model without learning its complexities. With a few functions, you can copy / download and generate a MultiAssayExperiment from the TCGA example workspaces provided by Terra.

• tomoseqr tomoseqr is an R package for analyzing Tomo-seq data. Tomo-seq is a genome-wide RNA tomography method that combines combining high-throughput RNA sequencing with cryosectioning for spatially resolved transcriptomics. tomoseqr reconstructs 3D expression patterns from tomo-seq data and visualizes the reconstructed 3D expression patterns.

• TREG RNA abundance and cell size parameters could improve RNA-seq deconvolution algorithms to more accurately estimate cell type proportions given the different cell type transcription activity levels. A Total RNA Expression Gene (TREG) can facilitate estimating total RNA content using single molecule fluorescent in situ hybridization (smFISH). We developed a data-driven approach using a measure of expression invariance to find candidate TREGs in postmortem human brain single nucleus RNA-seq. This R package implements the method for identifying candidate TREGs from snRNA-seq data.

• UCell UCell is a package for evaluating gene signatures in single-cell datasets. UCell signature scores, based on the Mann-Whitney U statistic, are robust to dataset size and heterogeneity, and their calculation demands less computing time and memory than other available methods, enabling the processing of large datasets in a few minutes even on machines with limited computing power. UCell can be applied to any single-cell data matrix, and includes functions to directly interact with SingleCellExperiment and Seurat objects.

• updateObject A set of tools built around updateObject() to work with old serialized S4 instances. The package is primarily useful to package maintainers who want to update the serialized S4 instances included in their package. This is still work-in-progress.

• xcore xcore is an R package for transcription factor activity modeling based on known molecular signatures and user’s gene expression data. Accompanying xcoredata package provides a collection of molecular signatures, constructed from publicly available ChiP-seq experiments. xcore use ridge regression to model changes in expression as a linear combination of molecular signatures and find their unknown activities. Obtained, estimates can be further tested for significance to select molecular signatures with the highest predicted effect on the observed expression changes.

New Data Experiment Packages

There are 5 new data experiment packages in this release of Bioconductor.

• crisprScoreData Provides an interface to access pre-trained models for on-target and off-target gRNA activity prediction algorithms implemented in the crisprScore package. Pre-trained model data are stored in the ExperimentHub database. Users should consider using the crisprScore package directly to use and load the pre-trained models.

• epimutacionsData This package includes the data necessary to run functions and examples in epimutacions package. Collection of DNA methylation data. The package contains 2 datasets: (1) Control ( GEO: GSE104812), (GEO: GSE97362) case samples; and (2) reference panel (GEO: GSE127824). It also contains candidate regions to be epimutations in 450k methylation arrays.

• healthyControlsPresenceChecker A function that reads in the GEO accession code of a gene expression dataset, retrieves its data from GEO, and checks if data of healthy controls are present in the dataset. It returns true if healthy controls data are found, and false otherwise. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL https://ftp.ncbi.nlm.nih.gov/geo/series/.

• VectraPolarisData Provides two multiplex imaging datasets collected on Vectra instruments at the University of Colorado Anschutz Medical Campus. Data are provided as a Spatial Experiment objects. Data is provided in tabular form and has been segmented and phenotyped using Inform software. Raw .tiff files are not included.

• xcoredata Provides data to use with xcore package.

New Annotation Packages

There are 8 new annotation packages in this release of Bioconductor.

• BSgenome.Cjacchus.UCSC.calJac4 Full genome sequences for Callithrix jacchus (Marmoset) as provided by UCSC (calJac4, May 2020) and wrapped in a BSgenome object.

• BSgenome.CneoformansVarGrubiiKN99.NCBI.ASM221672v1 Full genome sequences for Cryptococcus neoformans var. grubii KN99 (assembly ASM221672v1 assembly accession GCA_002216725.1).

• BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0 The T2T-CHM13v2.0 assembly (accession GCA_009914755.4), as submitted to NCBI by the T2T Consortium, and wrapped in a BSgenome object. Companion paper: “The complete sequence of a human genome” by Nurk S, Koren S, Rhie A, Rautiainen M, et al. Science, 2022.

• BSgenome.Mfascicularis.NCBI.6.0 Full genome sequences for Macaca fascicularis (Crab-eating macaque) as provided by NCBI (assembly Macaca_fascicularis_6.0, assembly accession GCA_011100615.1) and stored in Biostrings objects.

• JASPAR2022 JASPAR is an open-access database containing manually curated, non-redundant transcription factor (TF) binding profiles for TFs across six taxonomic groups. In this 9th release, we expanded the CORE collection with 341 new profiles (148 for plants, 101 for vertebrates, 85 for urochordates, and 7 for insects), which corresponds to a 19% expansion over the previous release. To search thisdatabases, please use the package TFBSTools (>= 1.31.2).

• MafH5.gnomAD.v3.1.2.GRCh38 Store minor allele frequency data from the Genome Aggregation Database (gnomAD version 3.1.2) for the human genome version GRCh38.

• SNPlocs.Hsapiens.dbSNP155.GRCh38 SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 155. The 948,979,291 SNPs in this package were extracted from the RefSNP JSON files for chromosomes 1-22, X, Y, and MT, located at https://ftp.ncbi.nih.gov/snp/latest_release/JSON/ (these files were created by NCBI on May 25, 2021). These SNPs can be “injected” in BSgenome.Hsapiens.NCBI.GRCh38 or BSgenome.Hsapiens.UCSC.hg38.

• UCSCRepeatMasker Store UCSC RepeatMasker AnnotationHub resource metadata. Provide provenance and citation information for UCSC RepeatMasker AnnotationHub resources. Illustrate in a vignette how to access those resources.

New Workflow Packages

There are no new workflow packages.

New Books

There are no new online books.

NEWS from new and existing Software Packages

ADaCGH2

             Changes in version 2.35.1 (2022-04-19)                 

• Added required code from ffbase (as ffbase no longer in CRAN) (ffbase authors added to authors’ list). ffbase no longer a dependency.

affxparser

             Changes in version 1.67.1 (2022-03-23)                 

SIGNIFICANT CHANGES

• This packages requires R (>= 4.0.0) when build on MS Windows. This is due to the added support for UCRT on MS Windows, which is required for the upcoming R 4.2.0.

SOFTWARE QUALITY

• Updates to build package from source on MS Windows with UCRT. Thanks to Tomas Kalibera for the contribution.

• Now registering native routines - apparently never happened before.

             Changes in version 1.67.0 (2021-10-27)                 
  

• The version number was bumped for the Bioconductor devel version, which is now BioC 3.15 for R-devel.

airpart

                    Changes in version 1.3.4                        

• Paper published in Bioinformatics…

alevinQC

                   Changes in version 1.11.1                        

• Added support for reading alevin-fry output

AlpsNMR

             Changes in version 3.5.1 (2022-04-07)                  

• plot_interactive now accepts an overwrite argument to avoid asking the user interactively
• Improve nmr_detect_peaks_tune_snr to tune the SNR threshold with the right other parameters
• Documentation improvements
• Split Peak_detection page into smaller and more specific pages
• Let the user choose how code is parallellized, as suggested by BiocParallel documentation.
• Replace furr/future parallellization loops with BiocParallel. Provides a warning in case a future::plan() has been set.
• Demote Imports to Suggests: SummarizedExpriment, S4Vectors, ggrepel, GGally
• Remove dependencies: tidyselect, assertthat, plyr, furrr
• Add download_MTBLS242() function to help download the data for the tutorial
• Skip mixOmics test if affected by https://github.com/mixOmicsTeam/mixOmics/pull/199
• Fix auto setting of the baseline threshold for the peak detection

AnnotationHub

                    Changes in version 3.3.0                        

NEW FEATURES

• (3.3.6) Serialized S4 hub resources (AnnotationHub and ExperimentHub) are now passed thru updateObject() at load-time

USER-VISIBLE MODIFICATIONS

• (3.3.8) Add instructions for creating a hub shared across multiple users

• (3.3.2) Remove TESTING option as only needed to expose devel orgdb

• (3.3.2) Change filter for orgdbs. orgdbs at release time will be stamped with devel (to be release) and then manually have biocversion added for the upcoming new devel. Filtering then based on biocversion number. This will expose devel orgdbs as soon as generated

BUG CORRECTION

• (3.1.9) Fix broken test. Identical not appropriate. all present appropriate

AnnotationHubData

                   Changes in version 1.25.0                        

SIGNIFICANT UPDATES

• 1.25.7 Update recipes to upload to azure. NonStandardOrgDb release recipe updated

• 1.25.6 Update recipes to upload to azure. TwoBit ensembl and release recipes for standard TxDb and OrgDb updated

NEW FEATURES

• 1.25.5 Add helper function to upload to azure

MODIFICATIONS

• 1.25.2 Changed makeAnnotationHubMetadata to point to Azure instead of AWS

AnVIL

                    Changes in version 1.8.0                        

NEW FEATURES

• (v 1.7.4) add avworkflow_configuration_*() functions for manipulating workflow configurations, and a vignette describing use.

• (v 1.7.5) add avdata_import() to import ‘REFERENCE DATA’ and ‘OTHER DATA’ tables.

• (v 1.7.9) export repository_stats() to summarize binary package availability.

USER VISIBLE CHANGES

• (v 1.7.4) Deprecate avworkflow_configuration(), avworkflow_import_configuration().

• (v 1.7.4) Update Dockstore md5sum.

• (v 1.7.5) avdata() is re-implemented to more faithfully report only ‘REFERENCE DATA’ and ‘OTHER DATA’ workspace attributes; previously, other attributes such as the description and tags (from the workspace landing page) were also reported.

BUG FIXES

• (v 1.7.4) avworkflow_files() and avworkflow_localize() do not fail when the workflow has produced no files.

• (v 1.7.6) improve handling of authentication token for gcloud utilities.

                   Changes in version 1.7.13                        
  

BUG FIXES

• Correct gcloud_project() when user environment variable set. https://github.com/Bioconductor/AnVIL/pull/52

                    Changes in version 1.6.6                        
  

BUG FIXES

• Correct gsutil_pipe() argument mis-match, see https://support.bioconductor.org/p/9141780/

APAlyzer

             Changes in version 1.9.4 (2022-02-28)                  

• Fixed typos in vignettes

             Changes in version 1.9.3 (2022-02-27)                  
  

• Fixed the issues caused by the lastest ensembl GRCm39 GTF.

• Fixed typos in vignettes

             Changes in version 1.9.2 (2022-01-02)                  
  

• Added supporting of multi-condition design in APAdiff.

             Changes in version 1.9.1 (2021-11-28)                  
  

• Added MultiTest parameter for APAdiff.

• Improved the performance and fixed issues in PAS2GEF.

• Update documents and authorships.

aroma.light

             Changes in version 3.25.1 (2022-04-21)                 

BUG FIXES

• Fixed partial argument name used in iwpca().

ATACseqQC

                   Changes in version 1.19.3                        

• fix the email typo.

                   Changes in version 1.19.2                        
  

• Change the method to fix the issue that NA is generated for conservation scores when call gscores.

                   Changes in version 1.19.1                        
  

• Fix the issue that NA is generated for conservation scores when call gscores.

atena

             Changes in version 1.2.0 (2022-04-21)                  

USER VISIBLE CHANGES

• Higher accuracy in TE quantification for TEtranscripts and Telescope methods.

• Improved EM step running time.

• New AnnotationHub resource has been added: UCSCRepeatMasker.

• Implemented function to retrieve and parse TE annotations.

AUCell

                    Changes in version 1.17                         

• New function: AUCell_run()

• Support for DelayedArray and Sparse matrices

BANDITS

                   Changes in version 1.11.1                        

• “prior_precision” function made faster (prior computation based on a sub-set of the genes only)

bandle

                   Changes in version 1.0.0                       

version 0.99.8

• minor bioc changes

version 0.99.7

• speed up package compiling
• fixing compiling issues

version 0.99.6

• fix pointer to self in compiled code

version 0.99.5

• remove timeout issues

version 0.99.4

• fix bioconductor review suggestions

version 0.99.2

• bioconductor stable version initialized

version 0.0

• initial package commit

BASiCS

             Changes in version 2.7.1 (2021-11-03)                  

• Add FixNu argument to fix scaling parameters to scran normalisation factors when WithSpikes=FALSE

• Exclude features with absolute estimates of fold change/difference less than the DE threshold when performing differential expression analysis with BASiCS_TestDE.

BayesSpace

                    Changes in version 1.5.1                        

Minor improvements and fixes

• Update readVisium to work properly when feature names include whitespaces
• Fix rounding of w_i sum in MCMC

• Add details to vignette related to spatialEnhance

                    Changes in version 1.5.0                        
  

New Bioconductor devel (3.15)

• Version numbering change with Bioconductor version bump

BEclear

             Changes in version 2.11.1 (2022-03-31)                 

• replaced dependency outliers with dixonTest

beer

             Changes in version 0.99.8 (2022-02-14)                 

• Fixed minor bugs with outdated arguments in the vignette.

             Changes in version 0.99.7 (2022-02-14)                 
  

• Changed bp.param argument to be called BPPARAM to be consistent with BiocParallel arguments.

             Changes in version 0.99.6 (2022-02-09)                 
  

• Corrected future reference in README to BiocParallel

• Changed ordering of arguments to put those without defaults first.

             Changes in version 0.99.3 (2022-01-31)                 
  

• Documentation
  • Corrected typos, formatting errors, and missing links.
  • Modified DESCRIPTION to include URL and remove Collates
  • Removed directions for installing PhIPData in the README and Vignette.
  • Added package citations for edgeR.
  • Added package man page.
  • Additional details have been added to the documentation for phipseq_model.bugs.
  • Added citation.
• Code
  • Standardized function names to use camelCase.
  • Standardized function arguments to use dot.case.
  • Though edgeROne() and brewOne() are not meant to be directly interfaced by the user, the two function names have been changed to reflect that they are still exported.
  • Renamed edgeR() to runEdgeR() to be more descriptive.
  • Corrected paste0() that should have been file.path().

  • Converted to BiocParallel from future for parallelization support.

             Changes in version 0.99.0 (2022-01-13)                 
    

• Submitted to Bioconductor

benchdamic

             Changes in version 1.1.1 (2021-03-21)                  

• Corrected a bug in DA_ALDEx2 function

• Updated DA_ALDEx2 function manual

• Added more authors in the citation

             Changes in version 1.1.0 (2021-10-26)                  
  

• Bump x.y.z version to odd y following creation of RELEASE_3_14 branch

BindingSiteFinder

                    Changes in version 1.1.2                        

• coverageOverRanges() can be allowed to produce NAs for uneven ranges in the output

                    Changes in version 1.1.1                        
  

• coverageOverRanges() matches the order of input ranges and output matrix for options merge_all_replicates and merge_replicates_per_condition

bioCancer

                   Changes in version 1.23.03                       

• host cgdsr

                   Changes in version 1.23.02                       
  

• Update NEWS

                   Changes in version 1.23.01                       
  

• get cgdsr from github

BiocCheck

                    Changes in version 1.32                         

NEW FEATURES

• Add package metadata to main report for easier diagnostics

• <pkgname>.BiocCheck folder, created above the package folder, includes the full report and NAMESPACE suggestions, if available.

• Add check to find any stray <pkgname>.BiocCheck folders

• Update doc links and recommendations for additional information in report

• Update BiocCheck report to be more brief by only noting the conditions; details are included in the full report

BUG FIXES AND MINOR IMPROVEMENTS

• Initialize default verbose value (FALSE) for internal reference object

• Flag only hidden ‘.RData’ files as bad files and allow ‘myData.RData’ (@hpages, #155)

• Improve internal handling of condition messages with unified mechanism

• Internal improvements to BiocCheck mechanism: export .BiocCheck object which contains all conditions, log list, and method for writing to JSON

• Update to changes in R 4.2 --no-echo flag

• Make use of lib.loc to helper functions that install and load the checked package

• (1.31.36) Reduce function length count slightly by removing empty lines.

• (1.31.35) Restricted files in inst will be flagged with a WARNING instead of an ERROR

• (1.31.32) Account for S3 print methods when checking for cat usage

• (1.31.31) Single package imports in the NAMESPACE were breaking the code to get all package imports.

• (1.31.29) Include other import fields from NAMESPACE file when checking consistency between imports in DESCRIPTION/NAMESPACE.

• (1.31.27) Update and clean up unit tests.

• (1.31.26) Improve load test for the package being checked.

• (1.31.25) Exclude GitHub URLs that end in HTML from external data check.

• (1.31.23) Internal updates to the require and library check.

• (1.31.22) Remove old code related to running BiocCheck on the command line and update BiocCheck documentation.

• (1.31.21) Remove redundant = from message to avoid = assignment.

• (1.31.20) Add line feed to “Checking function lengths…” message

• (1.31.18) Packages should not download files when loaded or attached.

• (1.31.17) Using ‘=’ for assignment should be avoided and ‘<-‘ should be used instead for clarity and legibility.

• (1.31.16) Note the use of cat and print outside of show methods.

• (1.31.15) Check for pinned package versions in the DESCRIPTION file denoted by the use of ==.

• (1.31.14) Enhancements to internal helper functions and BiocCheckGitClone

• (1.31.13) Revert move to new package checks. Update Bioc-devel mailing list check to fail early when not in BBS environment.

• (1.31.12) Move Bioc-devel mailing list and support site registration checks to new package checks.

• (1.31.10) Various internal improvements to BiocCheck and the identification of the package directory and name.

• (1.31.6) Use a more reliable approach to identify package name from the DESCRIPTION file.

• (1.31.5) Fixed bug in the case where the VignetteBuilder field in the a package’s DESCRIPTION has more than one listed.

• (1.31.3) Add BioCbooks repository url to checkIsPackageNameAlreadyInUse, VIEWS file is pending.

• (1.31.2) Fix logical length > 1 error in checkImportSuggestions (@vjcitn, #141)

• (1.31.1) Simplify check for function lengths; remove excessive dots.

BiocFileCache

                     Changes in version 2.3                         

ENHANCEMENT

• (2.3.4) Add instructions for a shared cache across multiple users of a system

• (2.3.2) Add direct SQL calls for certain retrieval functions to speed up access time. This will speed up the bfcquery function as well as any function tha utilized the underlying .sql_get_field, .get_all_rids or .get_all_web_rids.

• (2.3.1) Add @LTLA solution for making bfcrpath thread safe

BioCor

                   Changes in version 1.19.1                        

• Added alternative text to plots on vignettes.
• Reactivated again the comparison with GOSemSim

BiocParallel

                    Changes in version 1.30                         

USER VISIBLE CHANGES

• (v 1.29.1) Report first remote error in its entirety. https://github.com/Bioconductor/BiocParallel/issues/165

• (v 1.29.4) Add bpresult() (extract result vector from return value of tryCatch(bplapply(…))) and allow direct use of tryCatch(bplapply(…)) return value as arugment to bplapply(BPREDO= …). Closes #157

• (v 1.29.8) The default timeout for worker computation changes from 30 days to .Machine$integer.max (no timeout), allowing for performance improvements when not set.

• (v 1.29.11) The timeout for establishing a socket connection is set to getOption(“timeout”) (default 60 seconds).

• (v 1.29.15) Check for and report failed attempts to open SnowParam ports.

• (v 1.29.18) add bpfallback= option to control use of lapply() (fallback) when 0 or 1 workers are available.

• (v 1.29.19) add bpexportvariables= option to automatically export global variables, or variables found in packages on the search path, in user-provided FUN= functions.

BUG FIXES

• (v 1.29.2) Fix regression in use of debug() with SerialParam. https://github.com/Bioconductor/BiocParallel/issues/128

• (v 1.29.3) Fix regression in progress bar display with bplapply(). https://github.com/Bioconductor/BiocParallel/issues/172

• (v 1.29.5) Fix default seed generation when user has non-default generator. https://github.com/Bioconductor/BiocParallel/pull/176

• (v 1.29.9) Fix validity when workers, specified as character(), are more numerous than (non-zero) tasks. https://github.com/Bioconductor/BiocParallel/pull/181

BiocStyle

                   Changes in version 2.24.0                        

BUG FIXES

• Fixed incompatibility with recent versions of the longtable latex package when producing a PDF vignette. This bug manifested with the message ‘LaTeX Error: Missing \begin{document}.’ when attempting to knit. (https://github.com/Bioconductor/BiocStyle/issues/89)

biocViews

                   Changes in version 1.63.0                        

BUG FIX

• (1.63.1) Fix bug with Authors@R parsing for making VIEWS

biodb

             Changes in version 1.3.3 (2022-04-02)                  

• Explain how to use custom CSV file in vignette.

             Changes in version 1.3.2 (2022-03-11)                  
  

• Correct ext pkg upgrade: do not generate C++ example files again.

• Change default vignette name to package name.

• When upgrading a extension package, do not generate C++ files again.

• Accept an unknown total in Progress class.

• isSearchableByField() accepts field.type param now.

             Changes in version 1.3.1 (2021-12-10)                  
  

• Remove custom cache folder setting in vignette.

biodbChebi

             Changes in version 1.1.1 (2022-03-15)                  

• Change vignette name. Set author name.

• Remove code already in biodb package.

• Upgrade maintenance files.

biodbExpasy

             Changes in version 0.99.0 (2022-03-15)                 

• Submitted to Bioconductor

biodbHmdb

             Changes in version 1.1.2 (2022-03-13)                  

• Change vignette name.

• Update HMDB extract zip file used for vignette and testing.

biodbKegg

             Changes in version 1.1.1 (2022-03-17)                  

• Upgrade maintenance files.

• Correct instantiation example.

biodbLipidmaps

             Changes in version 1.1.1 (2022-03-17)                  

• Update maintenance files.

• Add log output to ouput file during check.

biodbMirbase

             Changes in version 0.99.1 (2022-04-01)                 

• Remove getNbEntries() example in vignette. No such web service exists in miRBase.

             Changes in version 0.99.0 (2022-03-22)                 
  

• Submitted to Bioconductor

biodbNcbi

             Changes in version 0.99.6 (2022-03-24)                 

• Corrected example inside vignette.

             Changes in version 0.99.0 (2022-03-17)                 
  

• Submitted to Bioconductor

biodbNci

             Changes in version 0.99.0 (2022-03-22)                 

• Submitted to Bioconductor

biodbUniprot

             Changes in version 1.1.1 (2022-03-17)                  

• Update maintenance files.

• Correct instantiation in example.

biomaRt

                   Changes in version 2.52.0                        

BUG FIXES

• Stop reporting message about the use of https when using useEnsembl() with a ‘version’ argument.

• Use virtualSchemaName provided by a Mart, rather than simply “default”. This caused issues with the Ensembl Plants Mart.

BiRewire

                   Changes in version 3.27.5                        

• Update support tsne-> Rtsne

                   Changes in version 3.27.1                        
  

• Added a constraint flag for excluding positive and negative arcs between two nodes

BridgeDbR

                    Changes in version 2.5.0                        

NEW FEATURES

• Updated to BridgeDb 3.0.13

BUG FIXES

• Small typo fix in a code example in the Vignette

bugsigdbr

                    Changes in version 1.2.0                        

• importBugSigDB accepts Zenodo DOIs and Github hashes to obtain defined data releases or devel to obtain the latest version (new argument version).
• Ontology-based queries for experimental factors and body sites (new functions getOntology and subsetByOntologies)
• Compilation of meta-signatures from individual signatures for one body site and one condition at a time, weighted by sample size (new function getMetaSignatures)

CAGEr

                    Changes in version 2.2.0                        

BUG FIXES

• Restore the correctSystematicG option in getCTSS(). See #61.

• Restore object class consistency in if / else statement in private function bam2CTSS. Fixes #49.

• Restore proper CTSS conversion from BAM files (bug introduced in v1.34.0) while fixing issue #36.

• Ensure Tag Clusters have a Seqinfo. Fixes #63.

CAMERA

                   Changes in version 1.51.1                        

USER VISIBLE CHANGES

• Move to mzML for example data and vignette following the removal of mzData support in mzR

canceR

                   Changes in version 1.29.03                       

• host cgdsr functions

                   Changes in version 1.29.01                       
  

• get cgdsr from github

cbaf

             Changes in version 1.18.0 (2022-04-24)                 

New Features

• Packge now uses cBioPortalData package to communicate with cBioPorta, as cgdsr package is deprecated.

• Package now supports RNA-seq data with z-scores relative to normal samples.

• Terms updated.

• Minor improvemets

CBEA

                   Changes in version 0.99.3                        

NEW FEATURES

• Created an output type object (CBEAout). This is an S3 type object that is essentially a list that incorporates the final score matrix as well as other diagnostic details.

SIGNIFICANT USER-VISIBLE CHANGES

• Due to the new feature above, now instead of getting a tibble, users would have to extract the scores out either using the provided function or use a custom approach based on the list-of-list format of the CBEAout objects.
• Implemented tidy and glance methods to deal with CBEAout objects

BUG FIXES

None

                   Changes in version 0.99.2                        

NEW FEATURES

• Added an option (parametric) to specify whether the null is estimated parametrically or via pure permutation. To support this, an option (n_perm) was also added to specify the number of permutations. A warning will be added if parametric is FALSE but n_boot is small (< 100)
• Added option (parallel_backend) to specify the parallel backend of the loop using BiocParallel
• Argument control now allow for a special slot titled fix_comp that can specify which component of the two-component mixture distribution to fix during the adjustment process.

SIGNIFICANT USER-VISIBLE CHANGES

• Combined raw argument with output argument for the CBEA function to specify returning raw CBEA scores (without any distribution fitting and transformation).
• New and revamped vignettes
• Significant reduction in dependencies, including removing native support for phyloseq

BUG FIXES

None

                   Changes in version 0.99.1                        

NEW FEATURES

None

SIGNIFICANT USER-VISIBLE CHANGES

None

BUG FIXES

• Removed .Rproj file to conform with Bioconductor error

                   Changes in version 0.99.0                        
  

NEW FEATURES

• Added a NEWS.md file to track changes to the package.
• Added a complete functionality to perform CBEA from scratch with bundled data set

SIGNIFICANT USER-VISIBLE CHANGES

None

BUG FIXES

None

cBioPortalData

                    Changes in version 2.8.0                        

New features

• Auth token string or file can now be included in the cBioPortal function.
• The check_build argument can be set to FALSE for alternative APIs, e.g., KidsFirst, when using cBioPortalData
• queryGeneTable translates gene IDs (‘hugoGeneSymbols’ <> ‘entrezGeneIds’) via the API service
• getDataByGenes supersedes getDataByGenePanel
• getStudies() replaces data(‘studiesTable’) to discover study IDs

Bug fixes and minor improvements

• Fixed issue where the by argument was not passed to getDataByGenes in internal calls
• Add names to metadata elements that originate from GISTIC datasets.

cbpManager

                    Changes in version 1.3.2                        

• Oncotree functionality is now avaliable also in the sample tab.
• Major modifications of the Mutation tab. Mutation data is now editable.

celda

             Changes in version 1.11.0 (2022-03-31)                 

• Improvments to decontX vignette
• Added ability to subsample to speed up perplexity calculations
• Added ability to use batch parameter with the raw matrix in decontX

ceRNAnetsim

             Changes in version 1.7.3 (2022-15-03)                  

• New functions, find_affected_nodes and find_targeting nodes

• Fixed test files

• Fixed documentations

ChIPpeakAnno

                   Changes in version 3.29.6                        

• update jianhong’s email

                   Changes in version 3.29.5                        
  

• update the pipeline documentation to avoid the error when converting the GRanges object to data.frame.

                   Changes in version 3.29.3                        
  

• handle the error “non standard bed file.”

                   Changes in version 3.29.2                        
  

• fix the error: trying to generate an object from a virtual class “DataFrame”.

                   Changes in version 3.29.1                        
  

• add subGroupComparison parameter to getEnrichedGO and getEnrichedPATH.

ChIPQC

                   Changes in version 1.31.2                        

• bugfixes

• handle larger plots

ChIPseeker

                   Changes in version 1.32.2                        

• update vignette

                   Changes in version 1.31.4                        
  

• readPeakFile now supports .broadPeak and .gappedPeak files (2021-12-17, Fri, #173)

                   Changes in version 1.31.3                        
  

• bug fixed of determining promoter region in minus strand (2021-12-16, Thu, #172)

                   Changes in version 1.31.1                        
  

• bug fixed to take strand information (2021-11-10, Wed, #167)

chromstaR

                   Changes in version 1.21.1                        

BUG FIXES

• Fixed ENSEMBL host for rnorvegicus_gene_ensembl. Using default host now instead of may2012.archive.ensembl.org.

CIMICE

                    Changes in version 1.3.1                        

Overview:

• Removed dependency with relations

ClassifyR

                    Changes in version 3.0.0                        

• Now supports survival models and their evaluation, in addition to existing classification functionality.

• Cross-validation no longer requires specific annotations like data set name and classifier name. Now, the user can specify any characteristics they want and use these as variables to group by or change line appearances. Also, characteristics like feature selection name and classifier name are automatically filled in from an internal table.

• Ease of use greatly inproved by crossValidate function which allows specification of classifiers by a single keyword. Previously, parameter objects such as SelectParams and TrainParams had to be explicitly specified, making it challenging for users not familar with S4 object-oriented programming.

• Basic multi-omics data integration functionality available via crossValidate which allows combination of different tables. Pre-validation and PCA dimensionality techniques provide a fair way to compare high-dimensional omics data with low-dimensional clinical data. Also, it is possible to simply concatenate all data tables.

• Model-agnostic variable importance calculated by training when leaving out one selected variable at a time. Turned off by default as it substantially increases run time. See doImportance parameter of ModellingParams for more details.

• Parameters specifying the cross-validation procedure and data modelling formalised as CrossValParams and ModellingParams classes.

• Feature selection can now be done either based a on resubstitution metric (i.e. train and test on the training data) or a cross-validation metric (i.e. split the training data into training and testing partitions to tune the selected features). all feature selection functions have been converted into feature ranking functions, because the selection procedure is a feature of cross-validation.

• All function and class documentation coverted from manually written Rd files to Roxygen format.

• Human Reference Interactome (binary experimental PPI) included in bundled data for pairs-based classification. See ?HuRI for more details.

• Performance plots can now do either box plots or violin plots. Box plot remains the default style.

cleanUpdTSeq

                   Changes in version 1.33.2                        

• Merge the codes by Haibo

                   Changes in version 1.33.1                        
  

• fix a bug for one line GRanges reported by Haibo

clusterProfiler

                    Changes in version 4.3.4                        

• fix enrichGO , gseGO and groupGO when keyType = ‘SYMBOL’ && readable=TRUE(2022-4-9, Sat)

                    Changes in version 4.3.3                        
  

• parse GAF file to prepare GO annotation data (esp for proteomic study) (2022-03-08, Tue, #397, #418, #421, #442)

• bug fixed in compareCluster() (2022-01-27, Thu, #424)

                    Changes in version 4.3.2                        
  

• bug fixed in extract_params() (2022-01-12, Wed, #392, @amcdavid)
• make simplify() works for gseGO() in compareCluster()

• support formula interface for GSEA methods in compareCluster() (2022-01-04, Tue, @altairwei, #416)

                    Changes in version 4.3.1                        
  

• compareCluster() supports GSEA algorithm (2021-12-11, Sat)
• update error message of download.KEGG.Path() and download.KEGG.Module()(2021-11-21, Sun)
• update simplify() function to support ont = ALL (2021-10-27, Wed)

clustifyr

             Changes in version 1.7.3 (2022-03-09)                  

• vec_out option for directly getting classification results as a vector, to be inserted into other metadata/workflow

• Maintainer change

CNVMetrics

                    Changes in version 0.1.6                        

NEW FEATURES

• calculateLog2ratioMetric() method enables log2 ratio metric calculation using similar workflow than calculateOverlapRegionsMetric() method.

SIGNIFICANT USER-VISIBLE CHANGES

• plotMetric() replaces plotOverlapMetric() method. The new method can plot all metrics (state call metrics and log2 ratio metrics).
• Vignette section ‘Workflow for metrics calculated using the level of amplification/deletion’ is complete.
• New citing section in README and vignette refering to published F1000Research poster (http://www.doi.org/10.7490/f1000research.1118704.1).
• Instead of calculating distance, log2 ratio metrics are calculated distance-based metrics (1/(1+distance)).

BUG FIXES

• None

                    Changes in version 0.1.4                        
  

NEW FEATURES

• None

SIGNIFICANT USER-VISIBLE CHANGES

• New website https://krasnitzlab.github.io/CNVMetrics/index.html associated to package.
• Vignette section ‘Workflow for metrics calculated using CNV status calls’ is complete.

BUG FIXES

• None

                    Changes in version 0.1.3                        
  

NEW FEATURES

• None

SIGNIFICANT USER-VISIBLE CHANGES

• plotOneOverlapMetric() method has a new argument silent=TRUE so that the plot is not drawn by default.

BUG FIXES

• plotOneOverlapMetric() method now uses sample distance for clustering as default clustering method.

                    Changes in version 0.1.2                        
  

NEW FEATURES

• plotOneOverlapMetric() method enables plotting result of overlapping metric calculation.

SIGNIFICANT USER-VISIBLE CHANGES

• calculateOverlapRegionsMetric() method changed to calculateOverlapMetric().

BUG FIXES

• None

                    Changes in version 0.1.1                        
  

NEW FEATURES

• Added a NEWS.md file to track changes to the package.
• calculateOverlapRegionsMetric() method enables calculation of similarity metrics using overlapping amplified/deleted regions.

SIGNIFICANT USER-VISIBLE CHANGES

• None.

BUG FIXES

• None

cola

                    Changes in version 2.1.1                        

• add hierarchical consensus partitioning

                    Changes in version 2.0.1                        
  

• predict_classes(): support svm/random forest methods for class label prediction.

coMET

             Changes in version 1.27.2 (2022-04-18)                 

• Update ENSEMBL functions for https

• Remove DNase_UCSC functions

• Add information about font.family for plotTrack and other Gviz functions

• Add showtext library in coMET.Rnw vignette

coMethDMR

                   Changes in version 0.99.9                        

We have been working on bug fixes and formatting/documentation changes as requested during the Bioconductor review. See these requests here: https://github.com/Bioconductor/Contributions/issues/2064

Breaking Changes

• In the CpGsInfoAllRegions(), CpGsInfoOneRegion(), and GetCpGsInRegion() functions, note that we have added a new argument region_gr (in the second position) which allows for the input of a GRanges object to these functions. This will cause errors in existing code if that code uses positional argument matching. Any existing code that matches arguments by name will be unaffected.

                   Changes in version 0.99.2                        
  

Major Changes

Bolstered documentation across all package help / manual files

Bug Fixes

                   Changes in version 0.99.1                        

Migrated all clean files to this repository. All development history in https://github.com/TransBioInfoLab/coMethDMR_old

                 Changes in version 0.0.0.9001                      

Major Changes

Included EPIC arrays annotation (#1) Added a check that: (#5) The rownames of the beta matrix are probe IDs, and There are only numeric columns in the beta matrix

Bug Fixes

compcodeR

                   Changes in version 1.31.1                        

• Implement simulations according to the phylogenetic poisson log normal model

• Implement length-varying simulations

• New PhyloCompData object for phylogenetic informed simulation data

• Add possible length normalization to DESeq2 and limma analyses

• Add phylolm analyses

ComplexHeatmap

                   Changes in version 2.11.1                        

• add a global option ht_opt$COLOR to control colors for continuous color mapping.

• annotation_label can be an expression object.

• recycle_gp(): now consider when n = 0.

• anno_block(): add align_to argument.

• add anno_text_box() and grid.text_box().

• add show_name argument in anno_empty().

• the validation of annotations in HeatmapAnnotation() is simplified.

• add anno_numeric().

• when rect_gp = gpar(type = "none"), use_raster is enforced to be FALSE.

• “global variables” outside cell_fun/layer_fun are aotumatially identified and saved locally.

CompoundDb

                    Changes in version 0.99                         

Changes in version 0.99.12

• Add mass2mz method for CompDb databases.

Changes in version 0.99.11

• Add peaksVariables method.

Changes in version 0.99.10

• Add parameter columns to peaksData.

Changes in version 0.99.9

• Add parameter dbFile to createCompDb and add an example on how to create a CompDb database from custom input.

Changes in version 0.99.8

• Add citation.

Changes in version 0.99.7

• Add bug reports link to DESCRIPTION.

Changes in version 0.99.6

• MsBackendCompDb extends Spectra::MsBackendCached instead of Spectra::MsBackendDataFrame.

Changes in version 0.99.5

• No updates, just version bump to cause a new build.

Changes in version 0.99.4

• Address more comments from @jianhong.

Changes in version 0.99.3

• Fix BiocCheck warnings.

Changes in version 0.99.2

• Fix BiocCheck warnings.

Changes in version 0.99.1

• Address comments/change requests from @jianhong.

Changes in version 0.99.0

• Preparing for Bioconductor submission.

                     Changes in version 0.9                         
  

Changes in version 0.9.4

• Add deleteIon and deleteSpectra allowing to delete ions or spectra.

Changes in version 0.9.3

• insertIons supports adding additional database columns.

Changes in version 0.9.2

• Add instertSpectra method to add MS/MS spectra from a Spectra object to the database.

Changes in version 0.9.1

• Add IonDb constructor methods.
• Expand documentation and examples.
• Add and fix unit tests.

Changes in version 0.9.0

• Add IonDb class as extension of CompDb (to allow adding ion information to the database) and the functionalities to create such object.
• Add insertIon to allow adding new ions to an IonDb object
• Add ionVariables, ions functions to access the ions data in the database.

• Add filters: IonIdFilter, IonAdductFilter, IonMzFilter, IonRtFilter.

                     Changes in version 0.8                         
  

Changes in version 0.8.1

• Import spectra type (MS level) and precursor type from MoNa.

Changes in version 0.8.0

• Rename database table name compound into ms_compound issue #74.

                     Changes in version 0.7                         
  

Changes in version 0.7.0

• Remove mass2mz and mz2mass function in favour of the functions implemented in MetaboCoreUtils.

                     Changes in version 0.6                         
  

Changes in version 0.6.6

• Import compounds method from ProtGenerics.

Changes in version 0.6.5

• Add parameter onlyValid to compound_tbl_sdf to allow importing of only valid elements issue #69.

Changes in version 0.6.4

• Add additional filters: MassFilter, FormulaFilter, InchiFilter and InchikeyFilter.

Changes in version 0.6.3

• Add metadata, spectraVariables and compoundVariables functions.

Changes in version 0.6.2

• Support creation of databases without specifying the organism.
• Ensure database columns are mapped correctly to Spectra variable names.

Changes in version 0.6.1

• Add SpectrumIdFilter to support filtering by spectrum IDs.

Changes in version 0.6.0

• Rename column names: compound_name -> name, mass -> exactmass, inchi_key -> inchikey.

                     Changes in version 0.5                         
  

Changes in version 0.5.0

• Replace as.list with peaksData.

• Replace asDataFrame with spectraData.

                     Changes in version 0.4                         
  

Changes in version 0.4.3

• Updated to match new LIPID MAPS field names.

Changes in version 0.4.2

• Fix bug in as.list,MsBackendCompDb which returned a SimpleList instead of a list.

Changes in version 0.4.0

• Rename method spectraData for MsBackendCompDb into asDataFrame (adapting to the changes in Spectra).

                     Changes in version 0.3                         
  

Changes in version 0.3.2

• Import also smiles from SDF files.

Changes in version 0.3.1

• Move package Spectra from Depends to Imports

Changes in version 0.3.0

• Change from MSnbase to RforMassSpectrometry packages (Spectra and MsCoreUtils).

• Store MS/MS spectra in two tables, msms_spectrum and msms_spectrum_peak.

                     Changes in version 0.2                         
  

Changes in version 0.2.3

• Add instrument and precursor_mz spectra data columns (issue #32).

Changes in version 0.2.2

• Add adduct information from Jan Stanstrup’s commonMZ package.
• Add matchWithPpm function to match numeric values allowing for a small difference.
• Add adducts function to retrieve adduct definitions.
• Add mass2mz and mz2mass to convert between mass and m/z for provided adducts.
• Add annotateMz method to annotate m/z values.

Changes in version 0.2.1

• Change field collision_energy to character to support values from MoNa (issue #31).
• Add functions import_mona_sdf and msms_spectra_mona functions to enable import of spectrum data from MoNa SDF files (issue #30).
• Add support for MoNa SDF files (issue #30).

Changes in version 0.2.0

• Add hasMz,Spectrum and hasMz,Spectra methods to look for m/z values within spectra (issue #28).
• Add MsmsMzRangeMinFilter and MsmsMzRangeMaxFilter (issue #29).
• Re-use Spectra object from MSnbase.

• Add supportedFilters,CompDb method.

                     Changes in version 0.1                         
  

Changes in version 0.1.1

• Add precursorMz, precursorCharge, precursorIntensity, acquisitionNum, scanIndex, peaksCount, msLevel, tic, ionCount, collisionEnergy, fromFile, polarity, smoothed, isEmpty, centroided and isCentroided methods for Spectrum2List.

Changes in version 0.1.0

• Add expandMzIntensity function.
• Add spectra method to extract spectra from the CompDb database.
• Add functionality to store MS/MS spectra in a CompDb database (m/z and intensity values stored as BLOB).
• Add functionality to load MS/MS spectra from HMDB xml files.

conclus

             Changes in version 1.3.4 (2022-03-28)                  

• Made the following significant changes
• Add parameter removeNoSymbol in the method normalizeCountMatrix to filter genes doesn’t have SYMBOL.
• clusterMarkers slot become topMarkers slot, accessors names change in the same way.0

CoreGx

                    Changes in version 2.0.0                        

• The @cell slot has become the @sample slot. Associated generics and accessor methods have been renamed, then aliased to their old names. As such, old code should still work as expected, but will in fact be calling different S4 methods.
• Added the @treatment slot to the CoreSet-class

COTAN

                   Changes in version 0.99.12                       

Release before the official release of Bioc 3.15. Main changes:

• The way in which the COEX matrix is estimated and stored is changed to occupy less space and run faster.

                   Changes in version 0.99.10                       
  

Initial Bioconductor release

crisprBase

                    Changes in version 1.0.0                        

• New package crisprBase, Base functions and classes for CRISPR gRNA design.

crisprBowtie

                    Changes in version 1.0.0                        

• New package crisprBowtie, Bowtie-based alignment of CRISPR gRNA spacer sequences.

crisprScore

                    Changes in version 1.0.0                        

• New package crisprScore, for on-target and off-target scoring of guide RNAs (gRNAs).

csdR

                    Changes in version 1.1.3                        

Added citation to the csdR article which is now printed.

                    Changes in version 1.1.2                        

Made it explicit in the documentation that missing values are not allows and wrote a test for this case.

                    Changes in version 1.1.1                        

Made some minor modifications to the README and the vignette.

customCMPdb

             Changes in version 1.5.1 (2022-01-31)                  

• Add DrugAge build 4 database

cytomapper

             Changes in version 1.7.2 (2022-04-20)                  

• Fixes for next release

             Changes in version 1.7.1 (2021-12-28)                  
  

• Added compImage function for channel spillover compensation

cytoMEM

             Changes in version 0.99.2 (2022-04-11)                 

• Updated show methods for build_heatmaps function

• Updated assignment from = to <-

             Changes in version 0.99.1 (2022-03-21)                 
  

• Updated class membership checks with is() and == / != to is(x, ‘class’) for S4 classes

• Version bump for Bioconductor

             Changes in version 0.99.0 (2022-03-18)                 
  

• Submitted to Bioconductor

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

dasper

                    Changes in version 1.5.1                        

NEW FEATURES

• Fix bug related to coverage_norm(), ensuring that regions used to normalise coverage have the same seqlevels as the inputted junctions.

dce

             Changes in version 1.3.5 (2022-04-14)                  

• Update package data df_pathway_statistics

dearseq

             Changes in version 1.7.2 (2022-04-13)                  

• reintroduced CompQuadForm::davies() as a longer alternative when the “saddlepoint” method in survey::pchisqsum() fails for computing quadratic form asymptotic p-values

             Changes in version 1.7.1 (2022-02-07)                  
  

• added a spaghetti plot functionality

decoupleR

                     Changes in version 2.2                         

Changes

• Changed example mat and net to toy examples.

• Changed test data to toy data.

                     Changes in version 2.1                         
  

Changes

• likelihood param is deprecated, from now on, weights (positive or negative) should go to the mor column of network. Methods will still run if likelihood is specified, however they will be set to 1.

• Added minsize argument to all methods, set to 5 by default. Sources containing less than this value of targets in the input mat will be removed from the calculations.

• Changed default behavior of the decouple function. Now if no methods are specified in the statistics argument, the function will only run the top performers in our benchmark (mlm, ulm and wsum). To run all methods like before, set statistics to ‘all’. Moreover, the argument consensus_stats has been added to filter statistics for the calculation of the consensus score. By default it only uses mlm, ulm and norm_wsum, or if statistics==’all’ all methods returned after running decouple.

• viper method:

• Now properly handles weights in mor by normalizing them to -1 and +1.

• ulm/mlm/udt/mdt methods:

• Changed how they processed the input network. Before the model matrix only contained the intersection of features between mat and network’s targets, now it incorporates all features coming from mat ensuring a more robust prediction. Prediction values may change slightly from older versions.

• Deprecated sparse argument.

• ora method:

• Now takes top 5% features as default input instead of 300 up and bottom features.

• Added seed to randomly break ties

• consensus method:

• No longer based on RobustRankAggreg. Now the consensus score is the mean of the activities obtained after a double tailed z-score transformation.

• Discarded filter_regulons function.

• Moved major dependencies to Suggest to reduce the number of dependencies needed.

• Updated README by adding:

• Kinase inference example
• Graphical abstract
• Manuscript and citation

• New vignette style

• Updated documentation for all methods.

New features

• Added wrappers to easily query Omnipath, one of the largest data-bases collecting prior-knowledge resources. Added these functions:

• show_resources: shows available resources inside Omnipath.
• get_resource: gets any resource from Omnipath.
• get_dorothea: gets the DoRothEA gene regulatory network for transcription factor (TF) activity estimation. Note: this version is slightly different from the one in the package dorothea since it contains new edges and TFs and also weights the interactions by confidence levels.

• get_progeny: gets the PROGENy model for pathway activity estimation.

• Added show_methods function, it shows how many statistics are currently available.

• Added check_corr function, it shows how correlated regulators in a network are. It can be used to check for co-linearity for mlm and mdt.

• Added new error for mlm when co-variables are co-linear (regulators are too correlated to fit a model).

Bugfixes

• wmean and wsum now return the correct empirical p-values.

• ulm, mlm, mdt and udt now accept matrices with one column as input.

• Results from ulm and mlm now correctly return un-grouped.

• Methods correctly run when mat has no column names.

deepSNV

             Changes in version 1.99.3 (2013-07-25)                 

Updates

• A few changes to shearwater vignette

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

Bugfixes

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

             Changes in version 1.99.2 (2013-07-11)                 
  

Updates

• Updated CITATION

• Added verbose option to bam2R to suppress output

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

Bugfixes

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

             Changes in version 1.99.1 (2013-06-25)                 
  

Updates

• Using knitr for prettier vignettes

• Including shearwater vignette

Bugfixes

• fixed issues with deletions in bf2Vcf()

• makePrior() adds background on all sites

             Changes in version 1.99.0 (2013-04-30)                 
  

Updates

• New shearwater algorithm

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

DEGreport

                   Changes in version 1.31.6                        

• Migrate gather to pitvot_longer

• Fix warning in melt in degcovariates

• Fix significants function, issue with !!!sym

                   Changes in version 1.31.3                        
  

• Fix error in example when using head after pipe

DelayedArray

                   Changes in version 0.22.0                        

DEPRECATED AND DEFUNCT

• The following stuff is now defunct after being deprecated in previous versions of the package:
  • blockGrid(): replaced with defaultAutoGrid()
  • rowGrid(): replaced with rowAutoGrid()
  • colGrid(): replaced with colAutoGrid()
  • multGrids(): replaced with defaultMultAutoGrids()
  • linearInd(): replaced with Mindex2Lindex()
  • viewportApply(): replaced with gridApply()
  • viewportReduce(): replaced with gridReduce()
  • getRealizationBackend(): replaced with getAutoRealizationBackend()
  • setRealizationBackend(): replaced with setAutoRealizationBackend()
  • RealizationSink(): replaced with AutoRealizationSink()

BUG FIXES

• Small tweak to updateObject() method for DelayedArray objects (see commit abcd154).

DepecheR

                   Changes in version 1.11.4                        

• sPLSDA function testing excluded from BioConductor, as it works locally, but fails at BioConductor.

             Changes in version 1.11.3 (2022-03-12)                 
  

• Bug fix in dColorPlot affecting character vectors and factors used as input.

             Changes in version 1.11.2 (2022-03-11)                 
  

• Searching for unidentified bug in test for dSlsda function.

             Changes in version 1.11.1 (2022-03-05)                 
  

• Bug fix in dColorPlot, solving problems with individual continuous vectors

• microClust, an internal function, has been updated to include the counting of donors in addition to median and mean calculations among the neighbors.

• The addition of nUniqueNeihgDons, in conjunction to the aforementioned change to the microClust function.

• Minor updates to dSplsda function testing, to hopefully remove the problem of intermittent problems in the testing on the Linux plaform.

DepInfeR

             Changes in version 0.99.7 (2022-04-05)                 

• Modify package based on the comments from the second round revision

             Changes in version 0.99.4 (2022-03-19)                 
  

• Modify package according to comments from Bioconductor team

             Changes in version 0.99.0 (2022-01-13)                 
  

• Submitted to Bioconductor

DEWSeq

             Changes in version 1.9.2 (2022-04-19)                  

• add function to filter read counts based on max. position count

DExMA

                    Changes in version 1.3.1                        

• missGenesImput function added

• SampleKnn imputation method for unmeasured genes added

DiffBind

                     Changes in version 3.6                         

• Change default spike-in normalization to NATIVE (TLE/TMM)

• Change spike-in normalization to use reference library sizes

• Fix bug involving Called columns in reports

• Maintain FRiP calculations

• Improve dba.plotProfile sample labels

• Fix issue with package:parallel

• Fix error/warning in dba.blacklist relating to non-matching chromosome names

• Update man page for dba.report to clarify how fold changes are reported when bNormalized=FALSE.

• Add some new test conditions to GenerateDataFiles.R

distinct

                    Changes in version 1.7.2                        

• differential testing allowed, even when 1 gene only is provided

                    Changes in version 1.7.1                        
  

• when removing nuisance covariates, the previous linear model was replaced with a linear mixed effect model with: i) fixed effects for the nuisance covariates, and ii) random effects for the samples. This properly accounts for the correlation structure of cells belonging to the same sample.

dittoSeq

                     Changes in version 1.8                         

• Minor Feature Add: ‘randomize’ option for ‘order’ input of ‘dittoDimPlot()’ and ‘dittoScatterPlot()’

DMRcate

                    Changes in version 2.8.1                        

• CITATION updated.

DOSE

                   Changes in version 3.21.2                        

• enable setReadable for compareCluster(GSEA algorithm) result(2021-12-13, Mon)
• update the default order of GSEA result (2021-12-09, Thu)

• if p.adjust is identical, sorted by abs(NES)

                   Changes in version 3.21.1                        
  

• upate DisGeNET and NCG data (2021-11-14, Sun)
• DisGeNET v7: 21671 genes, 30170 diseases and 1134942 gene-disease associations
• 194515 variants, 14155 diseases and 369554 variant-disease associations
• NCG v7: 3177 cancer genes, 130 diseases and 6095 gene-disease associations

edgeR

                   Changes in version 3.38.0                        

• New argument ‘keep.EList’ for voomLmFit() to store the normalized log2-CPM values and voom weights.

enrichplot

                   Changes in version 1.15.4                        

• update treeplot: support passing rel object to offset and offset_tiplab (2022-04-24, Sun)

                   Changes in version 1.15.3                        
  

• export `drag_network’ (2022-03-07, Mon)
• update cnetplot.enrichResult to be supported by drag_network(2022-3-6, Sun)
• add function drag_network to drag the nodes of networks (2022-2-25, Fri)
• fix a bug in goplot: goplot.gseaResult need setType slot instead of ontology slot (2022-2-22, Tue)

• return gg object instead of print it in dotplot.compareClusterResult() (2022-01-05, Wed, @altairwei, #160)

                   Changes in version 1.15.2                        
  

• add label_format_tiplab and label_format_cladelab parameters for treeplot(2021-12-24, Fri)
• support treeplot of compareCluster(GSEA algorithm) result(2021-12-13, Mon)
• support visualization of compareCluster(GSEA algorithm) result(2021-12-11, Sat)

• support scientific notation for gseaplot2(2021-12-4, Sat)

                   Changes in version 1.15.1                        
  

• fixed R check by importing utils

ensembldb

                   Changes in version 2.19.10                       

• Fix issue in getGeneRegionTrackForGviz if no transcript was found in the provided genomic range (issue https://github.com/jorainer/ensembldb/issues/132).

                   Changes in version 2.19.9                        
  

• seqlevelsStyle allows to provide a custom mapping data frame.

                   Changes in version 2.19.8                        
  

• Require package Biostrings in the coordinate mapping vignette.

                   Changes in version 2.19.7                        
  

• listColumns does no longer report columns from the metadata database table (issue https://github.com/jorainer/ensembldb/issues/128).

                   Changes in version 2.19.6                        
  

• Fixes in proteinToGenome.

                   Changes in version 2.19.5                        
  

• Add support for additional tx_is_canonical column and add TxIsCanonicalFilter (issue https://github.com/jorainer/ensembldb/issues/123).

                   Changes in version 2.19.4                        
  

• Fix issue with quotes in transcript names when importing transcript tables.

                   Changes in version 2.19.2                        
  

• Restore backward compatibility (issue https://github.com/jorainer/ensembldb/issues/122).

                   Changes in version 2.19.1                        
  

• Add database column tx_name to store the external transcript names.

• Update TxNameFilter to allow filtering on this database column.

ensemblVEP

                   Changes in version 1.37.0                        

• add support for Ensembl release 105

epialleleR

             Changes in version 1.3.6 (2022-02-16)                  

• significant speed-up (1.3.5)

• methylation patterns

             Changes in version 1.3.2 (2021-12-24)                  
  

• more efficient data handling (XPtr instead of Rcpp::wrap’ping)

EpiCompare

                 Changes in version 0.99.3

New Features

• New functions with examples/unit tests:
  • import_narrowPeak: Import narrowPeak files, with automated header annotation using metadata from ENCODE.\
  • gather_files: Automatically peak/picard/bed files and read them in as a list of GRanges objects.\
  • write_example_peaks: Write example peak data to disk.
• Update .gitignore

• Update .Rbuildignore

                 Changes in version 0.99.1
  

New features

• New parameter in EpiCompare:

  • genome_build: Specify the genome build, either “hg19” or “hg38”. This parameter is also included in plot_chromHMM, plot_ChIPseeker_annotation, tss_plot and plot_enrichment.

                 Changes in version 0.99.0
    

New Features

• EpiCompare submitted to Bioconductor.

epigraHMM

                    Changes in version 1.3.2                        

• Exporting function estimateTransitionProb to estimate transition probabilities from a sequence of states of a Markov chain

                    Changes in version 1.2.1                        
  

• Bug fix of output paths to handle paths with ‘.’

epimutacions

                   Changes in version 0.99.33                       

• Bugs and notes (if possible) fixed

                   Changes in version 0.99.0                        
  

• Submitted to Bioconductor

escape

                    Changes in version 1.4.1                        

• Version number and small edits for bioconductor compliance

• Removed singscore method

• Added UCell functions internally so they are compatible with Bioconductor

EWCE

                    Changes in version 1.3.3                        

New features

• method argument from orthogene::create_background and orthogene::convert_orthologs is now passed up as an argument to EWCE functions to give users more control. “homologene” chosen as default for all functions. “homologene” has fewer species than “orthogene” but doesnt need to import data from the web. It also has more 1:1 mouse:human orthologs.
• Include notes on mismatches between GitHub documentation and current Bioc release version.
• Allow bin_specificity_into_quantiles to set specificity matrix name produced.
• Merge GHA workflow yamls into one.

Bug fixes

• Add try({}) and error=TRUE to avoid “polygon edge not found” error in vignettes.

                    Changes in version 1.3.1                        
  

New features

• Major changes: Pull Request from bschilder_dev branch.
• All functions can now use lists and CellTypeDatasets (CTD) from any species and convert them to a common species (human by default) via orthogene.
• Automated CTD standardisation via standardise_ctd.
• Can handle (sparse) matrices.
• Can create CTD from very large datasets using DelayedArray object class.
• All functions automatically create appropriate gene backgrounds given species.
• More modular, simplified vignettes.
• Additional gene pre-filtering options (DESeq2, MAST, variance quantiles).
• New/improved plotting functions (e.g. plot_ctd).
• Added example bootstrapping enrichment results as extdata to speed up examples (documented in data.R). Accessed via EWCE::example_bootstrap_results().
• Replaced GHA workflow with check-bioc to automatically: run R-CMD checks, run BiocCheck, and rebuild/deploy pkgdown site.
• Parallelised functions:
• drop_uninformative_genes
• generate_celltype-data
• bootstrap_enrichment_test
• Added tests (multiple functions tests per file to reduce number of times ewceData files have to be downloaded):
• test-DelayedArray
• test-merge_sce
• test-get_celltype_table
• test-list_species
• test-run_DGE
• test-check_percent_hits
• Added function is_32bit() to all tests to ensure they don’t get run twice on Windows OS.
• Added GitHub Actions workflows:
• check-bioc-docker.yml: Runs CRAN/Bioc checks, rebuilds and pushes pkgdown website, runs and uploads test coverage report,
• dockerhub.yml: Builds Bioconductor Docker container with EWCE installed, runs CRAN checks and (if checks are successful) pushes container to neurogenomicslab DockerHub.
• Removed docs folder, as the documentation website comes from the gh-pages branch now, and is automatically built by GHA workflow after each push to main branch.
• Added new exported function fix_celltype_names to help with standardising celltype names in alignment with standardise_ctd.
• generate_bootstrap_plots_for_transcriptome: Now supports any species (not just mouse or human).
• Converts CTD and DGE table (tt) into output_species gene symbols.
• Automatically generates appropriate gene background.
• Faster due to now having the option to only generate certain plot types.
• Provide precomputed results from ewce_expression_data via new example_transcriptome_results function.
• Reduced build runtime and oversized vignettes by not evaluating certain code chunks.
• Prevent extended vignette from running entirely.
• @return documentation for internal functions.
• Added more installation checks to GHA.
• Fixed inconsistent naming of unit test files: test_ ==> test-
• Removed DGE args in drop_uninformative_genes for now until we run benchmarking to see how each affects the EWCE results.
• Make bootstrap_plots function internal.
• Add report on how orthogene improve within- and across-species gene mappings in extended vignette.
• Record extra info in standardise_ctd output:
• “species”: both input_species and output_species
• “versions”: of EWCE, orthogene, and homologene

exomePeak2

             Changes in version 1.7.0 (2022-04-20)                  

• Improved accuracy by introducing new computational models of GC content bias correction and IP efficiency correction.

• Improved peak calling stability by applying Poisson test under default setting.

• Read count method is improved.

• Multi-step functions and quantification mode are deprecated.

• Unnecessary function parameters are removed.

ExperimentHub

                    Changes in version 2.3.0                        

USER VISIBLE MODIFICATIONS

• (2.3.5) Update documentaion for shared hub across multiple users

ExperimentHubData

                   Changes in version 1.21.0                        

MODIFICATIONS

• 1.21.2 Changed makeExperimentHubMetadata to point to Azure instead of AWS

fastreeR

                    Changes in version 1.0.0                        

• New package fastreeR, Phylogenetic, Distance and Other Calculations on VCF and Fasta Files.

             Changes in version 0.99.7 (2022-04-02)                 
  

• Updates and corrections after the 1st Bioconductor review.

             Changes in version 0.99.6 (2022-03-26)                 
  

• Drop function dist2hist.

             Changes in version 0.99.5 (2022-03-25)                 
  

• Update vignette’s use of dist2hist.

             Changes in version 0.99.4 (2022-03-25)                 
  

• Update java backend (createHistogram).

             Changes in version 0.99.3 (2022-03-25)                 
  

• Update java backend.

             Changes in version 0.99.2 (2022-03-25)                 
  

• Update README.md to inform about JDK>=8 requirement.

• Update java dependencies (jfreechart-1.5.3).

             Changes in version 0.99.1 (2022-03-24)                 
  

• Update vignette to use BiocFileCache so that sample vcf and fasta downloads not get repeated needlessly.

             Changes in version 0.99.0 (2022-03-21)                 
  

• Submitted to Bioconductor.

fgsea

                   Changes in version 1.21.1                        

• fix a reproducibility problem (https://github.com/ctlab/fgsea/issues/110)

FindIT2

             Changes in version 1.0.3 (2021-12-29)                  

• fix bug when chrosome length is too small (calcRP_coverage function)

             Changes in version 1.0.2 (2021-11-23)                  
  

• fix bug when type in colData is factor (integtate_replicates function)

             Changes in version 1.0.1 (2021-11-09)                  
  

• simplify loadPeakFile function

fishpond

                    Changes in version 2.2.0                        

• New vignette demonstrating allelic analysis at isoform, TSS, or gene-level. See more details below.
• New import functions for equivalence class analysis of Salmon or alevin data, written by Jeroen Gilis. See salmonEC() and alevinEC() man pages.
• New plotAllelicGene() and plotAllelicHeatmap() functions for plotting results from allelic expression analysis.
• New makeTx2Tss() helper function for allelic analysis.
• Now importFromAllelicCounts() can take a GRanges object as the tx2gene argument, so that ranges will be distributed to the rowRanges of the output SummarizedExperiment.
• Adding shiftX argument to plotInfReps() for numeric x variable, to help with overplotting.
• Re-organized package for new pkgdown homepage: https://mikelove.github.io/fishpond

flowAI

                   Changes in version 1.25.3                        

• Added option to use IQR to make the flow rate check less sensitive.

flowSpecs

             Changes in version 1.9.2 (2022-02-15)                  

• Adding a hexBin parameter to the oneVsAllPlot function

• Adding the dependency hexbin.

             Changes in version 1.9.1 (2021-12-18)                  
  

• Introduction of a dirName parameter to the oneVsAllPlot function.

• Increased versatility for the madFilter function.

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.

fobitools

                    Changes in version 1.3.2                        

• Fix bugs in vignettes

FRASER

                    Changes in version 1.6.1                        

• Fixing quantile filtering defaults (#28)

• Require min expression in 5% instead of 95% of the samples

• Require min expression on both sides of the junction

• Align FRASER package with DROP pipeline (#24)

• Move temp directory from tempdir() to working directory getwd()

• Improve visualizations and Improve documentation

• Improve internal object validation

• Minor bugfixes

gdsfmt

                   Changes in version 1.32.0                        

UTILITIES

• optimize using the utilities of the Matrix package for sparse matrices

GeneNetworkBuilder

                   Changes in version 1.37.2                        

• Add layout button for htmlwidgets

                   Changes in version 1.37.1                        
  

• Fix the version issue of STRINGdb

GENESIS

                   Changes in version 2.25.5                        

• Add new test option “fastSMMAT” to assocTestAggregate.

                   Changes in version 2.25.4                        
  

• Fixed a bug in pcrelate when running with both multiple sample blocks and multiple cores

                   Changes in version 2.25.3                        
  

• Fixed a bug in assocTestSingle for computing saddle-point approximation (SPA) p-values for variants (i.e. when using test = Score.SPA) when the input null model is not a mixed models (i.e. when fitNullModel was run with cov.mat = NULL , or all variance components converged to 0) and the family = “binomial”

GeneTonic

                    Changes in version 2.0.0                        

New features

• GeneTonic now offers the possibility to upload a GeneTonicList at runtime. This makes it possible to use the app as a server-like dashboard, which runs by default on no dataset provided, and populates its components upon successfully providing the data as expected
• The GeneSpector functionality in the Welcome panel provides a means to explore any gene in the expression set, coloring and grouping by any experimental covariate of interest
• It is possible to enter a set of genes and genesets in the Bookmarks panel, and these can be doubled checked against the available features of the current GeneTonicList - this, combined to the upload functionality, makes it possible to easily compare different gtl objects
• The GeneTonic app has a button to export the currently provided dataset - regardless of the input format - as a GeneTonicList. This is especially useful if one is providing the individual components (dds, res_de, res_enrich, annotation_obj) and would like to obtain the correct serialized object
• gs_upset adds the possibility to represent the results of enrichment analyses as upset plots, with the option to decorate them with DE-related information

Other notes

• The manuscript about GeneTonic is now published on BMC Bioinformatics at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04461-5
• the citation item has been updated accordingly
• The jittered position in the gene_plot is now completely reproducible, by setting a seed internally in the jitter generating function

GenomeInfoDb

                   Changes in version 1.32.0                        

DEPRECATED AND DEFUNCT

• releaseName() is now defunct on GenomeDescription objects.

• Remove fetchExtendedChromInfoFromUCSC() and available.species(). Both were defunct in BioC 3.14.

GenomicAlignments

                   Changes in version 1.32.0                        

• No significant changes in this version.

GenomicDataCommons

                   Changes in version 1.20.0                        

New features

• gdcdata has an ellipses argument to download data from the legacy archive, e.g., legacy = TRUE (#84, @LiNk-NY)
• missing (is MISSING) and !missing (NOT MISSING) operations implemented for filtering queries, see vignette (#96, @LiNk-NY)
• gdc-client version can be validated against last known good version based on data release (#99, @LiNk-NY)

Bug fixes and minor improvements

• gdc_clinical uses readr::type_convert to handle columns with inconsistent types from the API.
• update examples in documentation and vignette based on new data release

GenomicFeatures

                   Changes in version 1.48.0                        

NEW FEATURES

• Add proteinToGenome() generic and methods. Loosely modeled on ensembldb::proteinToGenome().

• Add extendExonsIntoIntrons().

SIGNIFICANT USER-VISIBLE CHANGES

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

• makeTxDbFromGFF() and makeTxDbFromGRanges() now recognize and import features of type “gene_segment”, “pseudogenic_gene_segment”, “antisense_RNA”, “three_prime_overlapping_ncrna”, or “vault_RNA”, as transcripts. Note that, according to the Sequence Ontology, the “gene_segment” and “pseudogenic_gene_segment” terms are NOT offsprings of the “transcript” term via the is_a relationship but we still treat them as if they were because that’s what Ensembl does in their GFF3 files!

DEPRECATED AND DEFUNCT

• Add warning about FeatureDb-related functionalities no longer being actively maintained.

• disjointExons() is now defunct after being deprecated in BioC 3.13.

GenomicRanges

                   Changes in version 1.48.0                        

NEW FEATURES

• Add subtract() for subtracting a set of genomic ranges from a GRanges object. This is similar to bedtools subtract.

• Add ‘na.rm’ argument to makeGRangesFromDataFrame().

DEPRECATED AND DEFUNCT

• Remove the GenomicRangesList() constructor. This constructor got deprecated in BioC 3.10 and defunct in BioC 3.13.

BUG FIXES

• Make sure promoters() works on GPos objects.

GenomicScores

                    Changes in version 2.8.0                        

USER VISIBLE CHANGES

• Added support to the latest version 3.1.2 of gnomAD MAF data, stored in the package MafH5.gnomAD.v1.1.2.GRCh38.

BUG FIXES

• Bugfix on a problem caused by unordered input genomic ranges of width larger than 1, whose result was return in the wrong order; see https://github.com/rcastelo/GenomicScores/issues/18

• Bugfix when accessing multiple populations of scores stored on an HDF5 backend.

GenomicSuperSignature

                    Changes in version 1.4.0                        

• [Bug Fix]
  • findStudiesInCluster: single-element clusters return the correct study now, instead of null
• [Major]
  • findStudiesInCluster: the output includes PC number of the participating study in the cluster and the variance explained by them. With studyTitle=FALSE, the output will be a data frame, not a character vector.
  • subsetEnrichedPathways: the new argument include_nes is added. If it is set to TRUE, the output will include NES from GSEA.
  • getRAVInfo and getStudyInfo: two new functions to extract basic metadata for RAVs and studies, respectively.
  • We characterize RAVs that are harder to interpret with the currently available information associated with them (more detail can be found bit.ly/RAVmodel_characterization). For the following functions, any output including those RAVs will have a defulat message: meshTable, drawWordcloud, heatmapTable, validatedSignatures. You can snooze this by setting filterMessage = FALSE
  • New required parameter RAVmodel for the following functions: annotatePC,heatmapTable and validatedSignatures.
  • New accessor version is available to check the version of RAVmodel
  • New function availableRAVmodel will output the different versions of RAVmodels available for downloading now.
  • getModel function now takes a new argument, version, to specify the version of RAVmodel to download.
• [Minor]
  • miniRAVmodel is updated

GenProSeq

             Changes in version 0.99.0 (2021-09-20)                 

• submission to Bioconductor

GeoDiff

                    Changes in version 1.1.2                        

• transfer maintainership

                    Changes in version 1.1.1                        
  

• change default values in fitNBth and NBthmDE wrapper functions to be consistent

                    Changes in version 1.1.0                        
  

• accepted by Bioconductor

GeomxTools

                   Changes in version 2.99.2                        

• documentation updates

                   Changes in version 2.99.1                        
  

• documentation updates

                    Changes in version 2.1.9                        
  

• documentation updates

                    Changes in version 2.1.8                        
  

• subset objects in tests & examples to decrease time

                    Changes in version 2.1.7                        
  

• coercions to Seurat and SpatialExperiment are S3 coercions

                    Changes in version 2.1.6                        
  

• added updateObject capability

                    Changes in version 2.1.5                        
  

New features:

• Handle multiple PKC file versions for a single module
• Only common probes in all versions for each module will be used
• Default behavior most recent PKC version for resolving probe assignments
• User can override default with a specified version file name

• Added SystematicName and GeneID from PKC to feature metadata

                    Changes in version 2.1.4                        
  

• Add code for grubbs test from deprecated outliers package

                    Changes in version 2.1.3                        
  

New features:

• Allow protein NGS experiment data reading

• New slot, analyte, added to refer to analyte type

                    Changes in version 2.1.2                        
  

Bug fixes:

• Bug fix in outlier testing

                    Changes in version 2.1.1                        
  

New features:

• Add coercion to Seurat and SpatialExperiment

                    Changes in version 2.1.0                        
  

• No changes from 1.1.4

GEOquery

                   Changes in version 2.63.2                        

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

ggmanh

                   Changes in version 0.99.0                        

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

ggmsa

                    Changes in version 1.1.4                        

updated the way smooth is invoked on simplot(2022-01-03, Mon)

added smoothed curve on simplot.(2021-12-17, Fri)

                    Changes in version 1.1.3                        

fixed the typo in “posHighligthed”, and changed it to snake_case “position_highlight” from camelCase “posHighligthed” (2021-12-13, Mon)

                    Changes in version 1.1.2                        

fixed the assignment error on line 155 ‘seqlogo.R’

                    Changes in version 1.1.1                        

fixed error: using

instead of

on 110 lines in geom_msa.R

ggtree

                    Changes in version 3.3.3                        

• geom_striplab() that supports aes() mapping (2022-04-22, Fri, #493)

• to.bottom parameter introduced in geom_hilight() to allow the highlight layer was added into the lowest layer stack (2022-04-22, Fri, #492)

                    Changes in version 3.3.2                        
  

• mv identify() method to ‘ggfun’ (2022-04-01, Fri)
• update identify.gg() to support ‘ggplot’ object and +xlim()

• update man files (2022-03-23, Wed, #489)

                    Changes in version 3.3.1                        
  

• use graph layouts to visualize tree (2021-12-10, Fri, #460, #461)
• igraph layout
• graphlayouts: https://cran.r-project.org/web/packages/graphlayouts/index.html
• scale_color_subtree and scale_colour_subtree to color subtree via taxa group information (e.g., cutree, or kmeans) (2021-12-01, Wed)
• set na.value = ‘white’ in msaplot() (2021-10-29, Fri)

ggtreeExtra

                    Changes in version 1.5.4                        

• set orientation argument automatically, when it is not be provided and the geom has the parameter. (2022-03-24, Thu)

                    Changes in version 1.5.3                        
  

• update the citation format. (2022-01-28, Fri)

                    Changes in version 1.5.2                        
  

• import geom_text , which was used in the axis of geom_fruit with do.call. (2021-11-24, Wed)

                    Changes in version 1.5.1                        
  

• update the lower limit of reference range in normalization precess. (2021-11-19, Fri)

GOSemSim

                   Changes in version 2.21.1                        

• Avoid eval-parse in load_OrgDb() (2022-01-10, Mon)

graphite

             Changes in version 1.41.2 (2022-04-21)                 

• Updated all pathway data.

GSVA

                    Changes in version 1.50                         

BUG FIXES

• Bugfix for https://github.com/rcastelo/GSVA/issues/54 to force filtering genes with constant expression behaving the same regardless of the delayed or non-delayed nature of the data container.

Harman

                   Changes in version 1.23.1                        

• Code syntax tweaks to remove warnings raised in later version of R.

• Increase the forceRand unit test from 10,000 to 30,000 iterations. This solves an occasional unit test failure due to sampling.

HDF5Array

                   Changes in version 1.24.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Improve error reporting in internal helper .h5openlocalfile()

BUG FIXES

• Make sure updateObject() handles very old HDF5ArraySeed instances.

hermes

                   Changes in version 0.99.4                        

• Corrected authors.

                   Changes in version 0.99.2                        
  

• First public release of the hermes package.
• Submission to BioConductor.

Miscellaneous

• New utility function cut_quantile for cutting a numeric vector into quantiles.
• New utility function cat_with_newline for concatenating and printing with newline.
• New check function check_proportion which checks for a single proportion.
• Better legends on the genes barplot and the correlation heatmap.

• Improved vignette layout using the BioConductor style.

                    Changes in version 0.1.1                        
  

New Features

• New function draw_scatterplot to produce scatterplots of two genes or gene signatures.
• New function draw_boxplot for boxplots of gene expression values.
• New function draw_barplot for barplots of dichotomized gene expression counts into two or three percentile categories.
• New helper function wrap_in_mae that wraps a single SummarizedExperiment object into an MAE object.
• New method rename that makes renaming columns of rowData and colData as well as assay names in existing SummarizedExperiment objects much easier, as a step before converting to HermesData.
• New method lapply that allows user to apply a function on all experiments in a MultiAssayExperiment.
• New method isEmpty that checks whether a SummarizedExperiment object is empty.
• New gene filtering option n_top in the calc_pca function, which allows filtering genes with greatest variability across samples.
• New class GeneSpec for specification of genes or gene signatures, see ?gene_spec for simple construction. Inclusion of gene signature functions colPrinComp1 and colMeanZscores to supplement standard column statistics functions.
• New helper function col_data_with_genes which extracts the sample variables saved in colData together with selected gene information as a combined data set.
• New helper function inner_join_cdisc which joins genetic with CDISC data sets.

Bug Fixes

• normalize() now also works when the hermes package is not loaded, i.e. you can use it with hermes::normalize().
• correlate() now also works when there are factor variables in the sample variables of the HermesData object.
• add_quality_flags() does no longer return NA as the technical failure flags for the samples if there is only a single gene contained in the input, but instead a vector of FALSE to ensure correct downstream functionality.

Miscellaneous

• Updated LICENCE and README with new package references.
• The multi_assay_experiment now contains HermesData experiments, different patient IDs, one experiment with normalized assays, and multiple samples per patient in one experiment.
• The main HermesData example is now saved in the package as hermes_data, and the previous summarized_experiment is still available. Note that patient IDs have been changed in the new version to align with the multi_assay_experiment.
• Renaming of required rowData and colData columns to be more consistent with standards and use lowercase snake-case names.
• Annotation querying and setting is now more flexible in that it also allows to query more annotations than the required ones.
• Instead of gene starts and ends, the total length of gene exons is now used as the annotation column size. Corresponding queries from BioMart are used to return this gene size.
• df_char_to_factor has been deprecated (and can still be used with a warning) and replaced with df_cols_to_factor, which also converts logical variables to factor variables.

• When providing SummarizedExperiment objects containing DelayedMatrix assays to the HermesData() constructor, these are silently converted to matrix assays to ensure downstream functionality.

                    Changes in version 0.1.0                        
  

• First internal release of the hermes package, which contains classes, methods and functions to import, quality-check, filter, normalize, and analyze RNAseq counts data for differential expression.
• hermes is a successor of the rnaseqTools R package. The core functionality is built on the BioConductor ecosystem, especially the SummarizedExperiment class. New users should first begin by reading the “Introduction to hermes” vignette to become familiar with the hermes concepts.

New Features

• Import RNAseq count data into the hermes ready format.
• Annotate gene information from the Ensembl database via biomaRt.
• Add quality control (QC) flags to genes and samples.
• Filter and subset the data set.
• Normalize the counts.
• Produce descriptive plots.
• Perform principal components analysis.
• Produce a templated QC Rmd report.
• Perform differential expression analysis.

HIBAG

                   Changes in version 1.32.0                        

• fix the issue on Win32 because of using deprecated tbb::task_scheduler_init

                   Changes in version 1.30.2                        
  

• require GCC >= v8.0 for compiling the AVX-512VPOPCNTDQ intrinsics

• fix hlaGDS2Geno() when loading a SeqArray GDS file

HiCDCPlus

             Changes in version 1.3.1 (2022-01-23)                  

• Fixed bug that prevents using different window sizes on TopDom

hpar

                    Changes in version 1.37                         

Changes in version 1.37.1

• Update to HPA release 21.0 <2021-11-22 Mon>

HPAStainR

             Changes in version 1.4.1 (2021-11-23)                  

• Quick fix for inclusion of

HPiP

             Changes in version 1.1.1 (2021-11-29)                  

• Updated the vignette examples
• Added clustering detection algorithms

HubPub

             Changes in version 1.3.0 (2021-11-24)                  

• Update CreateAHubPackageVignette to use Azure instead of AWS

• Update AzureStor for auth_header

idr2d

                    Changes in version 1.8.1                        

• added grid to Imports

• fixed citation

• updated DOI

IgGeneUsage

             Changes in version 1.9.3 (2022-03-31)                  

• input data checks extended

illuminaio

             Changes in version 3.24.0 (2021-05-19)                 

• The version number was bumped for the Bioconductor release version, which is now BioC 3.13 for R (>= 4.0.3).

             Changes in version 3.22.0 (2020-10-27)                 
  

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

             Changes in version 0.37.0 (2021-10-27)                 
  

• The version number was bumped for the Bioconductor devel version, which is now BioC 3.15 for R-devel.

imcRtools

             Changes in version 1.1.9 (2022-04-19)                  

• Bug fix: patchDetection now works on SpatialExperiment object

• Fix for release

             Changes in version 1.1.8 (2022-04-03)                  
  

• Adjusted read_cpout function to newest pipeline

             Changes in version 1.1.7 (2022-03-30)                  
  

• readSCEfromTXT: only read in last metal occurrence in .txt file name

             Changes in version 1.1.6 (2022-01-12)                  
  

• Bug fix: correctly index graphs when reading in steinbock data

             Changes in version 1.1.5 (2022-01-07)                  
  

• More specific access of metal tags

             Changes in version 1.1.4 (2021-12-23)                  
  

• Added option to restrict the maximum distance between neighbors in delaunay triangulation

             Changes in version 1.1.3 (2021-12-15)                  
  

• Bug fix: divide number of interactions by total number of cells for classic and patch interaction counting

             Changes in version 1.1.2 (2021-11-28)                  
  

• Moved all helper functions to single script

             Changes in version 1.1.1 (2021-11-16)                  
  

• Bug fix in testInteractions: consider now all possible combinations of cell types

immunoClust

                   Changes in version 1.27.6                        

• CHANGES

  • bugfix in default scales

                   Changes in version 1.27.5                        
    

• NEW FEATURES

  • Default-Scale for immunoMeta-objects

                   Changes in version 1.27.4                        
    

• CHANGES

  • problems with immunoMeta-objects with 1 cluster

                   Changes in version 1.27.3                        
    

• CHANGES
  • fixed problems with NA values in FCS data

  • default BD plot scales removed from meta.process

                   Changes in version 1.27.2                        
    

• CHANGES

  • class and parameter information added to methods weights and mu

                   Changes in version 1.27.1                        
    

• NEW FEATURES
  • added method cells for immunoClust-object
  • improvement in plot.immunoMeta
  • for.sample option in events.immunoClust

infercnv

             Changes in version 1.11.2 (2022-02-03)                 

• Sort observation groups names when storing the list of indices so they are plotted in order, making it easier to change the sorting on the final figure.

• Fix plotting error on Windows by adding a check that bitmapType option is not null before checking what it is to prevent error in comparison.

• Fix for some group labels being cut off in width at the bottom of the figure

• Add conversion of expression data in sparse matrix format to dense matrix when splitting references in n groups as parallelDist does not handle them.

             Changes in version 1.11.1 (2021-11-08)                 
  

• Link “plot_chr_scale” and “chr_lengths” options from plot_cnv() to run().

• Added parameter k_obs_group to plot_per_group so that it can be applied to each of the subsequent group plotting calls if desired.

• Added a check to plot_cnv when using the dynamic_resize option that the increased size is not above the max size allowed when using Cairo as the graphical back end on Linux. If it is, set the size to the highest allowed instead.

• Replaced all calls to dist() with parallelDist(num_threads). (suggestion from @WalterMuskovic)

• Updated the code to run the Leiden clustering to be able to handle bigger datasets (work around R not having long vectors implemented) and be more efficient.

• Add a warning to infercnv object creation if the number of cells is more than half of the setting for scientific notation in R, as it may cause an issue while using as.hclust(phylo_obj) in the Leiden subclustering step.

• Updated plot_cnv method and imports to handle sparse matrices.

• Fix main heatmap drawing which in some cases caused the plotting to be out of field in the output.

• Fix method that compares arguments with backups with changes in R 4.1.1

             Changes in version 1.10.1 (2021-11-08)                 
  

• Fix missing colnames in subcluster information when using the Leiden method (used downstream by add_to_seurat).

• Fix “plot_per_group” to handle infercnv objects with NULL clustering information (mainly to be able to plot using existing results but changing the annotations).

InPAS

                    Changes in version 2.3.1                        

• merge changes made by Haibo.

InteractiveComplexHeatmap

                    Changes in version 1.3.1                        

• depends on a more recent version of ComplexHeatmap.

• fixed the control icons when compact = TRUE.

• add two columns of “row_label” and “column_label” in the output of selectPosition(), selectArea(), selectByLabels().

• makeInteractiveComplexHeatmap(): add two new arguments: show_cell_fun/show_layer_fun which controls whether show graphics made by cell_fun/layer_fun on the main heatmap.

• default_click_action(): numbers show three non-zero digits.

• htShiny(): add app_options argument.

InterCellar

             Changes in version 2.2.0 (2022-04-06)                  

• Updated paper citation in README file

IntEREst

                   Changes in version 1.20.0                        

NEW FEATURES

• limitRanges parameter in interest() and interest.sequential() functions allow for targetted analysis. It only loads reads that map to the dfined coordinates.

IRanges

                   Changes in version 2.30.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Like the DataFrame class defined in the S4Vectors package, classes SimpleDataFrameList, CompressedDataFrameList, SimpleSplitDataFrameList, and CompressedSplitDataFrameList, are now virtual. This completes the replacement of DataFrame with DFrame announced in September 2019. See: https://www.bioconductor.org/help/course-materials/2019/BiocDevelForum/02-DataFrame.pdf

ISAnalytics

             Changes in version 1.5.4 (2022-04-20)                  

MAJOR CHANGES

• ISAnalytics has now a new “dynamic vars system” to allow more flexibility on user inputs, view the dedicated vignette with vignette(“workflow_start”, package=”ISAnalytics”)
• All package functions were reviewed to work properly with this system

NEW FEATURES

• gene_frequency_fisher() is a new function of the analysis family that allows the computation of Fisher’s exact test p-values on gene frequency - fisher_scatterplot() is the associated plotting function
• top_targeted_genes() is a new function of the analysis family that produces the top n targeted genes based on the number of IS
• NGSdataExplorer() is a newly implemented Shiny interface that allows the exploration and plotting of data
• zipped examples were removed from the package to contain size. To compensate, the new function generate_default_folder_structure() generates the standard folder structure with package-included data on-demand
• transform_columns() is a new utility function, also used internally by other exported functions, that allows arbitrary transformations on data frame columns

MINOR CHANGES

• remove_collisions() now has a dedicated parameter to specify how independent samples are identified
• compute_near_integration_sites() now has a parameter called additional_agg_lambda() to allow aggregation of additional columns
• CIS_grubbs() now signals if there are missing genes in the refgenes table and eventually returns them as a df
• outlier_filter() is now able to take multiple tests in input and combine them with a given logic. It now also produces an HTML report.
• Several functions now use data.table under the hood
• Color of the strata containing IS below threshold can now be set in integration_alluvial_plot()

BUG FIXES

• Fixed a minor bug in import_Vispa2_stats() - function failed when passing report_path = NULL
• Fixed minor issue in circos_genomic_density() when trying to use a pdf device

DEPRECATED FUNCTIONS

• unzip_file_system() was made defunct in favor of generate_default_folder_structure()

• cumulative_count_union() was deprecated and its functionality was moved to cumulative_is()

             Changes in version 1.5.3 (2022-01-13)                  
  

MINOR CHANGES

• Added arguments fragmentEstimate_column and fragmentEstimate_threshold in HSC_population_size_estimate(). Slightly revised filtering logic.

• Updated package logo and website

             Changes in version 1.5.2 (2021-12-14)                  
  

NEW (MINOR)

• Added function to check for annotation problems in IS matrices

MINOR CHANGES

• Added argument max_workers in function remove_collisions()
• Updated default functions for aggregate_metadata()
• Added annotation issues section in import matrices report

FIXES

• Fixed minor issue in internals for file system alignment checks
• Fixed minor issue in internal call to import_Vispa2_stats() from import_association_file()

• Added safe computation of sharing in remove_collisions(): if process fails function doesn’t stop

             Changes in version 1.5.1 (2021-10-28)                  
  

FIXES

• Attempt to fix issues with parallel computation on Windows for some plotting functions

iSEEu

                    Changes in version 1.7.1                        

• Fix bug causing .setCachedCommonInfo() to cache NULL value for valid.rowdata.names information of DynamicMarkerTable panel instead of empty character vector.

IsoformSwitchAnalyzeR

            Changes in version 1.17.04 (2022-01-06)                 

• Update type: minor.

• Fixed a bug in 1.17.03

            Changes in version 1.17.03 (2022-01-06)                 
  

• Update type: minor.

• Version bump due to correction in stable branch causing the 1.15 -> 1.17 bump.

• Fixed date for the last update.

• Fixed a problem with the use of pairwiseAlignment in analyzeSwitchConsequences() that could cause jaccard similarities to be somewhat wrong.

• Fixed a problem with the switchPlot and transcriptPlot where the color of the transcript would be grey instead of red.

• Updates which prepare IsoformSwitchAnalyzeR for future updates

            Changes in version 1.17.02 (2021-10-01)                 
  

• Update type: minor.

• Various error message updates

• Fixed a problem where importGTF() could have seqLevel problems after removals.

• addORFfromGTF() was updated to give better error messages.

            Changes in version 1.17.01 (2021-09-01)                 
  

• Update type: minor.

• Version bump due to Bioconductor release.

• preFilter() now applies the gene expression cutoff to both conditions instead of the overall average.

• analyzePFAM() was updated to reflect recent updates to the tidyverse read_fwf function. It furhtermore now better distinguishes tap seperated and fixed with files.

karyoploteR

                    Changes in version 1.21.0

BUG FIXES

• Fixed wrong positioning of chromosome names in some edge cases (github issue #114).

• kpAddLabels now work on zoomed in regions (github issue #112).

kebabs

                   Changes in version 1.29.1                        

• fixed C++ code to work with newer version of Rcpp (enforced STRICT_R_HEADERS)

• updated URLs and DOIs (now requires R version >= 3.3.0)

                   Changes in version 1.29.0                        
  

• new branch for Bioconductor 3.15 devel

LACE

                     Changes in version 2.0                         

• Implementation of a more complete framework.

• Implementation of dynamic user interface.

limma

                   Changes in version 3.52.0                        

• New function readSampleInfoFromGEO().

• Allow the trend argument of eBayes() to specify a general variance covariate.

• More detailed checking and error messages when the object input to lmFit() is a data.frame.

• Improve checking for incorrectly specified contrasts argument in contrasts.fit().

lineagespot

             Changes in version 0.99.0 (2021-09-21)                 

• Submitted to Bioconductor

• Added a NEWS file to track changes of the package

LinTInd

                   Changes in version 0.99.1                        

Bugfixes

• Define the default parameters in IndelIdents()

• Cancels reading of unnecessary dependent packages

                   Changes in version 0.99.0                        
  

First built

• Submitted to Bioconductor

                 Changes in version 0.0.0.9000                      
  

NEWS.md setup

• added NEWS.md creation with newsmd

maftools

                   Changes in version 2.12.00                       

(GitHub master branch/BC 3.15 RC)

NEW FUNCTIONS

• gtMarkers, prepAscat, prepAscat_t, segmentLogR provides interface to copy number analysis with ASCAT.
• plotMosdepth and plotMosdepth_t processes output generated by Mosdepth and performs copy number analysis with DNAcopy
• cancerhotspotsAggr Aggregates cancerhotspots reports

ENHANCEMENTS

• Added support for plotting adjusted p-values in somaticInteractions. Issue: 813
• Added support for the protein structure BECN2 Issue: 696

MAGeCKFlute

                   Changes in version 1.99.0                        

• Avoid downloading reference files

• Perform enrichment analysis based on human pathways by default

MassSpecWavelet

             Changes in version 1.61.3 (2022-04-05)                 

• Add signal to Suggests. Replace sav.gol() with signal::sgolayfilt(). Closes #2

• Minor documentation improvements

             Changes in version 1.61.2 (2022-04-04)                 
  

• Remove xcms and caTools. Those are great packages but we don’t use them directly in MassSpecWavelet.

• Replace Sweave with RMarkdown vignette and update styles with BiocStyle

             Changes in version 1.61.1 (2022-04-01)                 
  

• Change Maintainer to Sergio Oller
• Add NEWS.md file
• Fix warning (error on R>=4.2) when cwt() has a matrix in the wavelet argument
• Fix warning due to partial matching of arguments inside cwt()
• Move waveslim from Depends to Suggests
• Make all calls to recommended packages qualified (e.g. sd -> stats::sd)
• Remove empty sections in man/ files.
• Register C routines

MatrixQCvis

             Changes in version 1.3.8 (2022-04-12)                  

• change unit tests after changing namespace in 1.3.7

             Changes in version 1.3.7 (2022-04-12)                  
  

• change namespace in module_measuredValues_missingValues.R

             Changes in version 1.3.6 (2022-04-08)                  
  

• set internally parameters (probs, batchColumn) in normalizeAssay and batchCorrectionAssay to default values when the parameters are NULL

             Changes in version 1.3.5 (2022-04-04)                  
  

• fix error message in cvFeaturePlot after updating packages

             Changes in version 1.3.4 (2022-02-10)                  
  

• fix bug in hoeffDValues for pivot_wider after updating tidyr (version 1.2.0)

             Changes in version 1.3.3 (2022-01-25)                  
  

• harmonize clustering method in distShiny for columns/rows

             Changes in version 1.3.2 (2021-12-09)                  
  

• add import of txt and xlsx files for function maxQuant

• change rounding in mosaic that the plot shows more detailed numbers

             Changes in version 1.3.1 (2021-12-01)                  
  

• use make.names for character vectors and colnames(colData(se)) in the functions for dimension reduction plot, drift plot, ECDF plot, mosaic plot, features along variable histogram, UpSet plot

• add method “log” in function transformationAssay

• add function spectronaut to upload spectronaut files

MBECS

                   Changes in version 0.99.13                       

• Adjusted SVD code to more straightforward implementation.

• Fixed variable ordering for LM-variance calculations.

                   Changes in version 0.99.12                       
  

• Reduced size of data-sets in testing procedures to stop unit-test timeouts.

• Added examples to data objects and reporting functions.

                   Changes in version 0.99.11                       
  

• Cleaned repository.

• GitHub Readme includes Installation instructions and brief workflow tutorial.

                   Changes in version 0.99.10                       
  

• Added BiocViews: ReportWriting, Visualization, Normalization and QualityControl.

• Inlcuded ‘importFrom’ for all ggplot2 functionality.

• Required packages now live in Imports section.

• Switched to ‘aes_string’ to remove visible binding NOTEs in plot functions.

• Included local variables to shut up the remaining NOTEs.

• Moved ‘match.arg’ choices to function heads.

• Moved code for generation of mock-up dummy-data from data-raw into the data.R file.

• Added testing for dummy data.

• Fixed highlighting in vignette.

• Fixed gray-area issue in box-plots.

                   Changes in version 0.99.8                        
  

• Included NEWS file.

• Added Bioconductor installation instructions in vignette.

• Added package man-page.

• Set lazyData to false.

• Added URL and BugReports fields to Description.

• Remove bapred and permute packages from suggest because they are no longer required.

• Also removed pals package, but included reference because I use the tableau color-scheme.

• All packages that are required for execution are now ‘Depends’ instead of ‘Suggests’.

• Revised vignette content, formatting and spelling for more convenient user experience.

• Fixed test for percentile normalization to actually test PN-function.

• Prelim report now checks if clr/tss transformed values are present prior to calculating them.

• Report-names/directories can now be changed from default by user.

• Reporting functions included in testing.

• Formatted code to adhere to 4-space indentation and 80 characters width requirements. For the most part.

• Included code for generation of dummy-data.

mbOmic

                    Changes in version 0.99.3

UPDATE MAIN CLASSES

• remove mbSet S4 class
• add Set virtual class
• add bSet and mSet extend to Set class

ADD NEW FUNCTIONS

• add function to identify enterotype

memes

                    Changes in version 1.2.5                        

• fixed error in ame_compare_heatmap_methods that triggers when plotting without providing a group argument.

                    Changes in version 1.2.4                        
  

• updated NAMESPACE to fix R CMD CHECK note.

                    Changes in version 1.2.3                        
  

• fixed a bug in importTomTomXML where tomtom list column would contain missing data if tomtom was run using multiple database sources as input.

                    Changes in version 1.2.2                        
  

• fixed a bug in runStreme causing failures on data import for STREME version >= 5.4.1

                    Changes in version 1.2.1                        
  

• fixed a bug in runStreme causing failures when using BStringSetLists as input

meshr

                    Changes in version 2.0.2                        

• CITATION was updated

metabCombiner

                    Changes in version 1.5.2                        

• Bug Fix in fit_model():

  • rtx & rty parameter issue resolved

                    Changes in version 1.5.1                        
    

• New function updateTables():
  • user changes to combinedTable report
  • inclusion of non-intersected features
• Changes in metabCombiner():
  • handling of missing features enabled (i.e. when update() is used)
  • new argument “impute”
  • rtOrder argument bug fix
• Changes in metabCombine():
  • new arguments “union” & “impute”
• Changes in fit_model/ fit_gam()/ fit_loess():
  • new arguments rtx & rty
• Changes in batchCombine():
  • new argument “union”
  • expected multiple (2 or more) datasets as input
  • end message added
• Changes in labelRows()/ reduceTable()/ labelRowParam()/ reduceTableParam():
  • new argument ‘useID’
  • ‘resolveConflicts’ and ‘remove’ set to TRUE in reduceTable()
• Changes to metabData objects:
  • “extra”” column count added to show() message
• Package functions updated to handle “group 0”

MetaboAnnotation

                    Changes in version 0.99                         

Changes in 0.99.15

• Highlight query and target spectra in different colors for validateMatchedSpectra.
• query and/or target of type SummarizedExperiment supported for Matched objects.
• MatchedSummarizedExperiment class removed.
• query and/or target of type QFeatures supported for Matched objects.
• Support SummarizedExperiment and QFeatures for both query and target parameters in matchValues.

Changes in 0.99.14

• Improve plotly-based mirror plots in validateMatchedSpectra.

Changes in 0.99.13

• Fix issue about matchedData not working for result objects of matchValues, Mz2MassParam and matchValues, Mz2MassRtParam (issue #69).

Changes in 0.99.12

• Update plotly-based mirror plots in validateMatchedSpectra.

Changes in 0.99.11

• Change matchMz into matchValues (issue #65).

Changes in 0.99.10

• Add validateMatchedSpectra for manual inspection and validation of an MatchedSpectra object.

Changes in 0.99.9

• Add setBackend for MatchedSpectra objects.

Changes in 0.99.8

• Add matchMz, Mz2MassParam and matchMz, Mz2MassRtParam. (issue #56).

Changes in 0.99.7

• Add formula matching functions.

Changes in 0.99.5

• Add parameter … to plotSpectraMirror.
• Definitions of “score”, “score_rt” changed to be the difference (with sign) between query and target m/z or retention time respectively.
• “ppm_error” becomes error without sign.

Changes in 0.99.4

• Add matches m/z error (variable “ppm_error”) to the Matched object returned by matchMz.

Changes in 0.99.3

• Address Herve’s comments.

                     Changes in version 0.2                         
  

Changes in 0.2.11

• Fix calculation of correct number of rows/columns of the plot in plotSpectraMirror.

Changes in 0.2.10

• Add parameter toleranceRt to CompareSpectraParam to enable retention time-based pre-filtering (issue #35).

Changes in 0.2.9

• Add support for manually defined adducts to Mass2MzParam (issue #41).

Changes in 0.2.8

• Add parameter THRESHFUN_REVERSE to MatchForwardReverseParam to allow filtering results on forward and reverse score (issue #37).

Changes in 0.2.7

• Performance improvement in matchSpectra if no precursor m/z filter is used (issue #38).
• Report number of matching peaks in matchSpectra,MatchForwardReverseParam (issue #36).

Changes in 0.2.6

• Fix bug in matchSpectra that was wrongly calculating the acceptable m/z difference if tolerance was > 0 (issue #34). Fix proposed by Hugo Varet (@hvaret).

Changes in 0.2.5

• Improve performance of matchMz.
• Rename queryColumn and targetColumn to queryColname and targetColname.

Changes in 0.2.4

• Support data.frame, DataFrame and matrix in matchMz.
• Add addMatches and filterMatches functions.

Changes in 0.2.3

• Fixes in MatchedSpectra.

Changes in 0.2.2

• Add MatchedSummarizedExperiment.

Changes in 0.2.1

• Rename TargetMass2MzParam to Mass2MzParam.

Changes in 0.2.0

• Add support for matching m/z against m/z and m/z in addition to retention times to matchMz.

MetaboCoreUtils

                     Changes in version 1.3                         

MetaboCoreUtils 1.3.8

• Support for heavy isotopes in countElements/pasteElements/calculateMass (issue #53).

MetaboCoreUtils 1.3.7

• Fix bug in containsElements function (issue #51).

MetaboCoreUtils 1.3.6

• Add functions for Kendrick mass defects.

MetaboCoreUtils 1.3.5

• Add missing unit tests.

MetaboCoreUtils 1.3.4

• Add calculateMass function.

MetaboCoreUtils 1.3.3

• Vectorized versions for chemical mass functions.

MetaboCoreUtils 1.3.2

• Function for conversion of migration time to effective mobility in CE-MS.

MetaboCoreUtils 1.3.1

• Add isotope detection functionality.

MetNet

             Changes in version 1.13.2 (2022-03-04)                 

• add function addSpectralSimilarity and allow to add a MS2 similarity matrix (contribution by Liesa Salzer)

• adjust the functions threshold and combine to be able to deal with MS2 similarities (contribution by Liesa Salzer)

• adjust the vignette to the changes imposed by the new function addSpectralSimilarity (contribution by Liesa Salzer)

             Changes in version 1.13.1 (2022-02-11)                 
  

• update unit tests, e.g. remove ggm for as.data.frame, set R=1000 for bayes

mia

                     Changes in version 1.3                         

• name change: testForExperimentCrossCorrelation to testExperimentCrossCorrelation

• getExperimentCrossCorrelation: Filtering disabled by default, option to suppress warnings

• bugfix: taxonomyTree gave error if taxa were agglomerated at highest level (taxa name mismatch)

• bugfix: subsampleCounts errors if no samples are found after subsampling

• added loadFromMetaphlan

• renamed calculateUniFrac to calculateUnifrac

• added na.rm option to getTopTaxa function

• bugfix: makeTreeSEFromPseq – orientation of assay is taken into account

• bugfix: getExperimentCrossCorrelation’s “matrix”” mode works with features named equally

• bugfix: getExperimentCrossCorrelation’s calculates correlations correctly with features named equally

• getExperimentCrossCorrelation name changed to getExperimentCrossAssociation

• getExperimentCrossAssociation: user’s own function supported, sort in mode == table enabled

• getExperimentCrossAssociation: added MARGIN & paired options, efficiency of algorithm improved

miaViz

                     Changes in version 1.3                         

• Bugfix for plotting functions to support sparseMatrix and other assay types (2021-12-31)

microbiome

             Changes in version 1.17.2 (2022-02-15)                 

• Bug fix error in transform when taxa_are_rows is FALSE

• Merge microbiomeutilites functionality
  • Convert phyloseq slots to tibbles
  • Combine_otu_tax joins otu_table and tax_table
  • Merged add_besthit a fine tuned version from format_to_besthit
  • Merged psmelt2 a fine tuned version from phy_to_ldf
  • Bug fix in transform method alr

• alr transformation added

             Changes in version 1.17.1 (2022-01-11)                 
  

• Fixed bug in plot_core

• bfratio function removed

microbiomeMarker

                    Changes in version 1.1.2                        

• Development version on Bioconductor
• Use 3rd version of testthat to fix test error (use expect_snapshot() rather than expect_known_ouput).
• Add two new arguments in plot_heatmap() scale_by_row and annotation_col to improve heatmap viaualization, #52.
• Set slot marker_table to NULL if no marker was identified.
• Add new import function import_picrust2() to import prediction functional table from PICRUSt2, and all DA functions support for PICRUSt2 output data.
• Keep color consistent between legend and plot in cladogram, #42.

• Add a new argument clade_label_font_size in plot_cladogram() to specify font size of clade label, #49.

             Changes in version 1.1.1 (2020-03-07)                  
  

• Add a para only_marker in plot_cladogram to specify whether only show the markers or all features in the cladogram.
• Fix a bug in run_test_multiple_groups(), error group names for enrich groups (2021-10-12, #48).
• Fix a bug in plot_abundance(), error var name of effect size in marker_table (2021-10-17, #47).

MicrobiotaProcess

                   Changes in version 1.7.11                        

• add mp_plot_diff_cladogram to plot the result of mp_diff_analysis. (2022-04-19)

                   Changes in version 1.7.10                        
  

• optimizing the mp_aggregate_clade and mp_balance_clade. (2022-04-13)

                    Changes in version 1.7.9                        
  

• add mp_cal_pd_metric to calculate the related phylogenetic diversity metrics. (2022-04-02) including NRI, NTI, PD, PAE, HAED, EAED, IAC.
• add mp_balance_clade to calculate the balance score of internal nodes according to their tip nodes abundances. (2022-03-22)
• add extract_binary_offspring to find the descendant tip/internal/all (with type parameter) nodes. (2022-03-17)
• add mp_aggregate_clade and mp_diff_clade to calculate and test the abundance (differential signals) of internal node according to their tip nodes abundance. (2022-03-16)
• add mp_select_as_tip and fix the bug of mp_diff_analysis with specific tip.level (not OTU) argument. (2022-03-02, Mon)
• fix the replace_na bug of new tidyr. (2022-03-04, Fri)
• update mp_import_metaphlan to better parse the output of MetaPhlAn2. (2022-03-11, Fri)

• update the mp_cal_abundance to return the tbl_df contained numeric type sample metadata. (2022-03-11, Fri)

                    Changes in version 1.7.8                        
  

• supporting multiple group names and supporting numeric type for .group of mp_plot_alpha. (2022-02-15, Tue)
• supporting multiple group names for .group of mp_plot_abundance when plot.group=TRUE. (2022-02-14, Mon)

• fix the width of mp_plot_abundance with geom=”flowbar”. (2022-02-01, Tue)

• related issue

                    Changes in version 1.7.7                        
  

• fix the bug about the constant variables within groups in lda of MASS (2022-01-27, Thu)

                    Changes in version 1.7.6                        
  

• fix the issue, that kingdom level of taxonomy information contains k__ or K__, which is unknown annotation in kingdom. (2021-01-14, Fri)

• add mp_extract_taxatree and mp_extract_otutree (alias of mp_extract_tree). (2022-01-14, Fri)

                    Changes in version 1.7.5                        
  

• add the message for the not integers in mp_cal_alpha. (2021-12-31, Fri)
• remove the features which variance of their abundance is zero before identify different taxa. (2021-12-28, Tue)
• add bar option in mp_plot_abundance, default is flowbar, the other options are bar and heatmap
• use corrected relative eigenvalues when the eigenvalues has negative values. (2021-12-27, Mon)
• add new distmethod from hopach. (2021-12-27, Mon)
• update tax_table without required phyloseq. (2021-12-20, Mon)

• update mp_diff_analysis to support the factor type group (.group specified). (2021-12-20, Mon)

                    Changes in version 1.7.4                        
  

• update taxatree<- and otutree<- which will extract the intersection between the tip labels of input treedata and the rownames of MPSE. (2021-12-14, Tue)
• add taxonomy<- for MPSE to assign the taxonomy information, which will be converted to taxatree automatically. (2021-12-14, Tue)
• add tax_table for MPSE and return taxonomyTable defined in phyloseq. (2021-12-14, Tue)

• update mp_import_metaphlan to better parse the output of MetaPhlAn2. (2021-11-30, Tue)

                    Changes in version 1.7.3                        
  

• update ‘mp_plot_abundance’ (2021-11-24, Wed)
• support heatmap by setting geom.
• .group supports multiple characters and .sec.group will be removed in the next version.
• update mp_plot_diff_res (2021-11-23, Tue)
• support otutree and taxatree class by setting tree.type.
• support multiple layout types of tree by setting layout.
• support adjusting the gap between panel and width of panel by setting offset.abun, pwidth.abun, offset.effsize, pwidth.effsize
• support whether display the relative abundance of group instead of sample by setting group.abun=TRUE or sample number > 50

• add mp_plot_diff_res to visualize the result of mp_diff_analysis. (2021-11-22, Mon)

                    Changes in version 1.7.2                        
  

• speed up the mp_cal_abundance, mp_cal_venn and mp_cal_upset with dtplyr. (2021-11-18, Thu)
• update the guide of x axis of ggside in mp_plot_ord. (2021-11-15, Mon)
• update mp_plot_abundance to visualize the abundance of taxonomy from high (bottom) to low (top). (2021-11-15, Mon)
• support multiple annotation rows or cols of heatmap of mp_plot_dist with .group=c(group1, group2), and add set_scale_theme to adjust the scale or theme of subplot of heatmap. (2021-11-10, Wed)
• fix the issue when the taxonomy info is removed with select. (2021-11-09, Tue)
• update print for MPSE class. (2021-11-09, Tue)
• update otutree<- for support phylo class. (2021-11-09, Tue)
• speed up the integration of mp_cal_dist result with action=”add”. (2021-11-09, Tue)

• update as.MPSE for biom class to support parsing the metadata of sample. (2021-11-09, Tue)

                    Changes in version 1.7.1                        
  

• fix the issue when using filter only return a assays contained one feature (nrow=1). (2021-11-05, Fri)
• fix the error of rownames<- when rownames of MPSE is NULL. (2021-11-04, Thu)
• update ‘message’ or ‘stop error message’ when the ‘Abundance’ cannot be rarefied in some functions, such as mp_cal_alpha, mp_cal_venn, mp_cal_upset, mp_cal_abundance and mp_cal_NRT_NTI. (2021-10-29, Fri)
• introduce .sec.group argument to specify the second group name in mp_plot_abundance, if it is provided, the nested facet will be displayed. (2021-11-02, Tue)

miloR

             Changes in version 1.3.1 (2022-01-07)                  

• Fix bug in findNhoodGroupMarkers to merge on gene IDs explicitly
• Fix bug in makeNhoods to include index cell in nhoods() matrix
• Introduce graph-based neighbourhood definition - allows full compatibility with graph-only batch correction and graphs constructed by third-party tools
• Introduce graph-based spatial FDR correction to obviate the need for any distance calculations
• Add vignette to describe the use and application of contrasts in testNhoods
• Patch to correct SpatialFDR with sparse nhoods where density is ~0

mirTarRnaSeq

             Changes in version 1.3.2 (2022-04-06)                  

• suggest SPONGE rather than import

             Changes in version 1.3.1 (2022-03-26)                  
  

• added support for SPONGE

mistyR

                    Changes in version 1.4.0                        

• Release version for Bioconductor 3.15. See changes for 1.3.x.

                     Changes in version 1.3                         
  

• Switched from Louvain to Leiden algorithm for community detection (requires igraph >= 1.2.7).
• The metamodel is now build by ridge regression. Intercept p-values are not calculated, the values are set to NA for backwards compatibility.
• Unique value error for cv folds is downgraded to warning.
• Prefix can be added to the column names generated by the fucntions add_juxtaview and add_paraview. This allows modeling the maker expression by its own juxtaview and paraview.

• Bug fixes.

                    Changes in version 1.2.1                        
  

• Fixed a separator issue in results aggregation and signature generation that might cause issues with variable names containing “_”.

MLP

                   Changes in version 1.43.1                        

• getGeneSets: add ‘Rhesus’ to ‘species’ (available only for ‘GOBP’, ‘GOMF’, ‘GOCC’ or ‘KEGG’)

MobilityTransformR

                    Changes in version 0.99                         

• Function for conversion of migration time to effective mobility in CE-MS.

• Submitted to Bioconductor

monaLisa

                    Changes in version 1.1.2                        

• added citation to the Bioinformatics publication

                    Changes in version 1.1.1                        
  

• added link to pre-print manuscript on biorXiv to README.md
• added warning to bin(…, minAbsX = val) if adjusted zero-bin breaks deviate more than 20% from val
• added doPlot argument to plotMotifHeatmaps to select if heatmaps should be plotted or just generated and returned
• added LICENSE.md file
• expanded monaLisa.Rmd vignette with illustration on how to do a binary or single set motif enrichment analysis
• expanded on collineairty in regression in the selecting_motifs_with_randLassoStabSel.Rmd vignette and the choice of parameter values in stability selection.
• updated the results.binned_6mer_enrichment_LMRs.rds and results.binned_motif_enrichment_LMRs.rds files stored in monaLisa under the current version of the package.

Motif2Site

                   Changes in version 0.99.5                        

• Resolve problem with overwriting BiocStyle in vignette

                   Changes in version 0.99.4                        
  

• Remove examples from data.Rd

                   Changes in version 0.99.3                        
  

• Adding help page data.Rd

                   Changes in version 0.99.2                        
  

• Update readme by Bioconductor installation instructions using BiocManager
• Update description by adding R>=4.1 as dependency
• Update description by adding BugReports link
• Update description by changing lazyDate to false
• Update Vignettes by fixing typos, abstract, and author
• Update Vignettes by using BiocStyle and keeping code lines under 80 character
• Improve coding style
• Fixing some of the build notes

• Adding Motif2Site.Rd with a complete example

                   Changes in version 0.99.1                        
  

• All HOX-mouse samples are replaced with FUR-Ecoli ones
• extdata folder size is 4 MB as E. coli data is much smaller
• Vignettes was updated by E. coli data
• Examples were updated by E. coli data
• README were updated by E. coli data

• The build time has been decreased substantially

                   Changes in version 0.99.0                        
  

• The first version of Motif2Site was submitted to Bioconductor

motifStack

                   Changes in version 1.39.4                        

• Change the fontfamily from ‘mono,Courier’ to ‘mono’ in vignettes.

                   Changes in version 1.39.3                        
  

• add XMatrix format for importMatrix.

                   Changes in version 1.39.2                        
  

• Accept scales for y-axis for logo when ic.scale is FALSE.

                   Changes in version 1.39.1                        
  

• Accept user defined x-axis for logo.

MouseFM

             Changes in version 1.4.2 (2022-02-28)                  

• Citation adapted

             Changes in version 1.4.1 (2021-11-13)                  
  

• Set biomaRt to url of archived version GRCm38 to be compatible with the package

• Citation added

MQmetrics

                    Changes in version 1.3.3                        

• Removed unused dependency.

                    Changes in version 1.3.2                        
  

• Reporthing the fixed Modifications if the mqpar.xml is present.

                    Changes in version 1.3.1                        
  

• Added median to the PlotAndromedaScore().
• Remove warnings from the vignettes.
• Now MQmetrics can read the mqpar.xml file. This one must be located on the same directory as the combined folder.
• Reporting the number of threads used by MaxQuant if found the mqpar.xml file.

msa

                   Changes in version 1.27.2                        

• applied patch to allow msa to work with the new Windows UCRT toolchain

                   Changes in version 1.27.1                        
  

• workaround for problems running texi2dvi() on R 4.2.0; those occurred during package checks when running some examples and the vignette code

• updated URLs and DOIs (now requires R version >= 3.3.0)

• fixed msaConvert() function to now work well with newer versions of the ‘ape’ package (now requires at least version 5.2)

                   Changes in version 1.27.0                        
  

• new branch for Bioconductor 3.15 devel

MSA2dist

             Changes in version 0.99.3 (2022-03-18)                 

Major changes

Minor improvements and bug fixes

• Fix RcppThread::LdFlags warning

             Changes in version 0.99.2 (2022-01-28)                 
  

Major changes

Minor improvements and bug fixes

• Added RcppThread::ProgressBar

             Changes in version 0.99.1 (2022-01-27)                 
  

Major changes

• Changed version number into 0.99.2

Minor improvements and bug fixes

• Changed URL links in DESCRIPTION

             Changes in version 0.99.0 (2021-12-22)                 
  

Major changes

• Changed version number into 0.99.1

• Changed name from distSTRING into MSA2dist

• Submitted to Bioconductor

Minor improvements and bug fixes

MsBackendMassbank

                     Changes in version 1.3                         

Changes in 1.3.5

• Add parameter columns to peaksData.

Changes in 1.3.4

• Import and use spectraVariableMapping method from Spectra.

Changes in 1.3.3

• Map comment to spectra variable.

Changes in 1.3.2

• Use in addition unit tests from the Spectra package.
• Add filterPrecursorMzValues and filterPrecursorMzRange.

Changes in 1.3.1

• MsBackendMassbankSql extends Spectra::MsBackendCached to re-use the general caching mechanism provided by that backend.

MsBackendMgf

                     Changes in version 1.3                         

Changes in 1.3.3

• Import coreSpectraVariables from Spectra.

Changes in 1.3.2

• Adapt the spectraVariableMapping to Spectra version >= 1.5.8.

Changes in 1.3.1

• Run additional unit test suits defined in Spectra.

MsBackendMsp

                    Changes in version 0.99                         

Changes in 0.99.4

• Import coreSpectraVariables from Spectra.

Changes in 0.99.2

• Small updates and changes.

Changes in 0.99.1

• Address review comments.

                    Changes in version 0.98                         
  

Changes in 0.98.2

• Vignette added.

Changes in 0.98.1

• Improve export method to support multi-value fields and user-provided mappings.

Changes in 0.98.0

• Add additional spectra variable mappings.
• Call unit tests from the Spectra package.

MsBackendRawFileReader

                     Changes in version 1.1                         

• Call the Spectra test suite.

• Add export snippet for MGF export in vignette file.

• Add .top_n peak list filter example in vignette file.

• Add test case for comparing .top_n(n=10) function with Proteome Discoverer Software v2.5 workflow using scan 9594.

• Change rawrr dependency to v1.3.5 to benefit from monoisotopic mZ values.

MsCoreUtils

                     Changes in version 1.7                         

MsCoreUtils 1.7.5

• Function bin gains parameter returnMids to choose whether or not bin mid-points should be returned in the result list.

MsCoreUtils 1.7.4

• Fix ppm to always return a positive value (issue #94).

MsCoreUtils 1.7.3

• Add citation.

MsCoreUtils 1.7.2

• Use Matrix::colSums() by default to handle sparce ‘Matix’ and ‘matrix’ adjacency matrices.

MsCoreUtils 1.7.1

• New aggregate_by_matrix() that uses an adjacency matrix to aggregate quantitative features.
• Set colnames to the outputs of aggregate_by_matrix() and aggregate_by_vector() to make sure that these are always set and not reply on the underlying function.

MsCoreUtils 1.7.0

• New Bioc devel version

MSnbase

                    Changes in version 2.21                         

Changes in 2.21.7

• Fix mz calculation in calculateFragments for neutral losses with a charge > 1 (see issue 573).

Changes in 2.21.6

• Allow different orientation of axis labels in image2 (see issue 571).

Changes in 2.21.5

• Adapt to changes in mzR version 2.29.3.

Changes in 2.21.4

• Add transformIntensity function for Chromatogram and MChromatograms objects.

Changes in 2.21.3

• Fix bug (issue #561).

Changes in 2.21.2

• Fix bug in compareChromatograms that creates a non-symmetric similarity matrix.

Changes in 2.21.1

• Change default for MSnbase fast load variable: set to TRUE also on macOS.

msPurity

                   Changes in version 1.21.2                        

• Fixes due to mz and intensity being named in columns for mzR and XCMS

• Fixes for connection{base} file() opening changes (no longer accept w+a in function in R v4.2)

• Update tests for the above

• Update a reference of grpid in averageXFragSpectra functions more explicit (no change in functionality)

• Typo fix in vignette

                   Changes in version 1.21.1                        
  

• Bugfix for frag4feature for XCMS 3 compatability https://github.com/computational-metabolomics/msPurity/pull/93

• Remove imports that are no longer used

MSstatsConvert

                    Changes in version 1.5.1                        

• Fixed bugs related to data types.
• Fixed bug that resulted in missing TechReplicate column in output.
• Added Philosopher converter.
• Added methods for MSstatsValidated objects.

MSstatsTMT

             Changes in version 2.2.7 (2022-02-18)                  

• Minor change: extend PhilosophertoMSstatsTMTFormat function to have multiple types of input

             Changes in version 2.2.6 (2022-02-14)                  
  

• Major change: add PhilosophertoMSstatsTMTFormat function as converter for outputs from Philosopher

             Changes in version 2.2.5 (2021-10-25)                  
  

• Minor change: add different point shape to dataProcessPlotsTMT as indicator of imputed values

             Changes in version 2.2.3 (2021-10-06)                  
  

• Minor change: fix the bug when df.prior is infinite

MuData

                   Changes in version 0.99.0                        

• submitted package to Bioconductor

MultiAssayExperiment

                   Changes in version 1.22.0                        

Bug fixes and minor improvements

• Add data(“miniACC”) to examples after removing lazy loading.
• Class definition prototypes defined for cleaner extensibility (@hpages, #306).
• Doc and internal improvments to MultiAssayExperimentToMAF
• synAssay and nonSynAssay now require exact assay names in MultiAssayExperimentToMAF

multiHiCcompare

             Changes in version 1.13.0 (2022-04-21)                 

• Match NEWS and DESCRIPTION versioning

MungeSumstats

                   Changes in version 1.3.18                        

New features

• Can now handle general remote sumstats not just IEU GWAS

• More column header mappings

                   Changes in version 1.3.17                        
  

New features

• Clean up of column header mapping file, including FREQUENCY given priority over MAF and addition of new CHR mappings.

                   Changes in version 1.3.15                        
  

Bug fixes

• Handle cases for multi-trait GWAS when P columns exists separate to the trait specific P value so that when renaming occurs there isn’t two P columns. Inputted P column will be renamed to ‘P_input’

• Issue where ‘check allele flip’ wasn’t running when the sumstats had all SNP IDs missing and incorrect direction of A1/A2 and effect columns has now been fixed.

                   Changes in version 1.3.14                        
  

New features

• liftover
• Now exported function.
• Added args for more user flexibility.
• Uses GenomeInfoDb::mapGenomeBuilds to standardise build names.
• Warns users when mapped builds do not match one of the conversion options.
• Choice to output as data.table or GRanges.
• Added units tests for exported version.
• standardise_sumstats_column_headers_crossplatform
• Exported as standardise_header while keeping the original function name as an internal function (they call the same code).
• Added unit tests for exported version.
• Added chunks to *Getting started` vignette
• liftover tutorial
• “Quick formatting” of headers and file formats.

Bug fixes

• check_pos_se: Remove extra message() call around string.
• check_signed_col: Remove extra message() call around string.
• write_sumstats

• Added extra round of sorting when tabix_index=TRUE because this is required for tabix.

                   Changes in version 1.3.13                        
  

New Features

• Additional mappings for CHR
• Make A1, A2 upper-case

Bug fixes

• Bug fix for dealing with imputing SNP ID when there are indels

                   Changes in version 1.3.11                        
  

New Features

• MungeSumstats can now handle Indels better. It will:
• Not impute the RS ID of a SNP for an Indel
• Not remove the Indel based on the RS ID not being present in the SNP ref dataset.
• Not remove the Indel if it has the same base-pair location as a SNP in the sumstats.
• Can now handle vcfs with extensions .vcf.tsv, .vcf.tsv.gz and .vcf.tsv.bgz

Bug fixes

• For non-bi-allelic SNP runs, no longer remove duplicated SNPs based on their base-pair position or their RS ID.

                    Changes in version 1.3.9                        
  

New Features

• Exported functions. Added examples and unit tests:
• compute_nsize
• standardise_sumstats_column_headers_crossplatform
• formatted_example
• New arguments:
• standardise_sumstats_column_headers_crossplatform: Added arg uppercase_unmapped to to allow users to specify whether they want make the columns that could not be mapped to a standard name uppercase (default=TRUE for backcompatibility). Added arg return_list to specify whether to return a named list (default) or just the data.table.
• formatted_example: Added args formatted to specify whether the file should have its colnames standardised. Added args sorted to specify whether the file should sort the data by coordinates. Added arg return_list to specify whether to return a named list (default) or just the data.table.
• Removed codecode.yml and _pkgdown.yml files (no longer necessary).
• Added Issues templates for Bugs and Feature requests.
• Added .datatable.aware=TRUE to .zzz as extra precaution.
• vcf2df: Documented arguments.
• Made v2 of hex sticker: inst/hex/hex.png

Bug fixes

• Regenerated the gh-pages branch after it accidentally got deleted.
• Remove temporary docs/ folder.
• Updated GitHub Actions.
• Updated Dockerfile so it doesn’t run checks (this is now take care of by the GHA workflow).
• Added Windows-specific folders to .Rbuildignore.

• Made to_GRanges.R and to_VRanges.R file names lowercase to be congruent with function names.

                    Changes in version 1.3.7                        
  

Bug fixes

• Bug in checking for bad characters in RSID fixed

                    Changes in version 1.3.6                        
  

New Features

• Columns Beta and Standard Error can now be imputed. However note that this imputation is an approximation so could have an effect on downstream analysis. Use with caution.

                    Changes in version 1.3.5                        
  

Bug fixes

• Flipping of Odds Ratio corrected (1/OR rather than -1*OR)

                    Changes in version 1.3.4                        
  

Bug fixes

• Issue downloading chain file resolved

                    Changes in version 1.3.3                        
  

New Features

• More mappings added to default mapping file.

                    Changes in version 1.3.2                        
  

Bug fixes

• Previously rsids with characters added (e.g. rs1234567w) would cause an error when checking for the rsid on the reference genome. This has been fixed and the correct rsid will now be imputed from the reference genome for these cases.

                    Changes in version 1.3.1                        
  

New Features

• import_sumstats: Create individual folders for each GWAS dataset, with a respective logs subfolder to avoid overwriting log files when processing multiple GWAS.
• parse_logs: New function to convert logs from one or more munged GWAS into a data.table.
• list_sumstats: New function to recursively search for local summary stats files previously munged with MungeSumstats.
• Added new dataset inst/extdata/MungeSumstats_log_msg.txt to test logs files.
• Added unit tests for list_sumstats and parse_logs.
• Added new Docker vignette.
• Updated GHA workflows using r_workflows.
• Remove docs/ folder as the website will now be pushed to the gh-pages branch automatically by new GHA workflow.
• Made documentation in README more clear and concise.
• Added checks for p-values >1 or <0 via args convert_large_p and convert_neg_p, respectively. These are both handled by the new internal function check_range_p_val, which also reports the number of SNPs found meeting these criteria to the console/logs.
• check_small_p_val records which SNPs were imputed in a more robust way, by recording which SNPs met the criteria before making the changes (as opposed to inferred this info from which columns are 0 after making the changes). This function now only handles non-negative p-values, so that rows with negative p-values can be recorded/reported separately in the check_range_p_val step.
• check_small_p_val now reports the number of SNPs <= 5e-324 to console/logs.
• Unit tests have been added for both check_range_p_val and check_small_p_val.
• parse_logs can now extract information reported by check_range_p_val and check_small_p_val.
• New internal function logs_example provides easy access to log file stored in inst/extdata, and includes documentation on how it was created.
• Both check_range_p_val and check_small_p_val now use #’ @inheritParams format_sumstats to improve consistency of documentation.

Bug fixes

• Reduced vignette sizes.
• Removed usage of suppressWarnings where possible.
• Deleted old .Rproj file and hidden folder (contained large files).
• Configured .Rproj so it doesn’t store large data files.
• Fix badger issues: https://github.com/GuangchuangYu/badger/issues/34

• Prevent test-index_tabix.R from running due to errors (for now).

                    Changes in version 1.3.0                        
  

New Features

• Version bump to align with Bioconductor release 3.14.

muscat

                    Changes in version 1.9.3                        

• bug fix in pbDS(): drop samples w/o any detected features, otherwise edgeR::calcNormFactors() fails when lib.size 0

                    Changes in version 1.8.1                        
  

• bug fix in prepSim(): removal of genes with NA coefficients was previously not propagated to the dispersion estimates

• bug fix in test-resDR.R: set ‘min_cells = 0’ to assure that everything is being tested, otherwise unit tests could fail

mzR

                   Changes in version 2.29.4                        

• Re-apply fix for compile error on clang by Kurt Hornik, closes #263

• Remove text in DESCRIPTION hinting at the RAMP wrapper for mzData removed in 2.29.3

                   Changes in version 2.29.3                        
  

• Update to Proteowizard 3_0_21263

• Removed RAMP backend, dropping ability to read mzData

• header always returns a data.frame even for a single scan.

                   Changes in version 2.29.2                        
  

• Cleanup in build files

                   Changes in version 2.29.1                        
  

• Pwiz backend partially re-written to avoid segfault on macOS (https://github.com/sneumann/xcms/issues/422).

NanoMethViz

                    Changes in version 2.2.0                        

• Added heatmap argument to plot_gene(), plot_region() and plot_granges(). This adds a read-heatmap to the plot.
• Added cluster_regions() function to perform k-means clustering on a table of genomic regions based on methylation profile.
• Added median averaging method for trends in plot_gene(), plot_region() and plot_granges(). This can be changed using the new avg_method argument, default is mean.
• Added filter_methy() function to create a filtered methylation file.
• Added region_methy_stats() to obtain average methylation fractions of specific regions.
• Added methy_to_edger() direct conversion wrapper around methy_to_bsseq() and bsseq_to_edger().
• Added palette argument to plot_gene(), plot_region() and plot_granges() to allow custom colour palettes.
• Fixed bsseq_to_edger() failing when regions argument was used.
• Fixed heatmaps not staying in a single column when more than 2 groups were present.

NanoStringNCTools

             Changes in version 1.3.1 (2022-01-12)                  

• Enable compatibility with Gen 2.5 RCCs

             Changes in version 1.3.0 (2021-10-26)                  
  

• Initial Bioconductor devel 3.14 version

ndexr

                   Changes in version 1.17.0                        

• UPDATE: Using the RCX package for working with networks. Deprecated 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()

nnSVG

             Changes in version 0.99.0 (2022-03-02)                 

• version for submission to Bioconductor

NormalyzerDE

                   Changes in version 1.13.2                        

• Fixed leastRepCount setting of zero for statistics report

nullranges

                    Changes in version 1.1.4                        

• Needed to drop features that have 0 width after trimming in bootRanges.

• Made the validity test for bootRanges only look for iter.

                    Changes in version 1.1.1                        
  

• Change to factor-Rle output for bootRanges to simplify the downstream plyranges.

NxtIRFcore

             Changes in version 1.1.1 (2022-01-11)                  

• Bugfix for NxtSE constructor.

• Bugfix for Consistency filter: previously an “average” filter was used, such that upstream / downstream filter triggers counted for 0.5, whereas it added 1.0 if both up/downstream filters were triggered. From 1.1.1 onwards, 1.0 is added when either upstream or downstream consistency filter is triggered.

• Added two new annotation-based filters: Terminus and ExclusiveMXE. See ?NxtFilter for details

• Annotated retained introns RI are defined by any intron that is completely overlapped by a single exon of any transcript. They are calculated as binary events, i.e. as PSI between RI and specific spliced intron, and do not consider overlapping splice events (unlike IR events, which are calculated for all other constitutive introns)

                    Changes in version 1.1.0                        
  

• Initial devel release for Bioconductor 3.15

OGRE

                   Changes in version 0.99.8                        

• added coverage plot

                   Changes in version 0.99.6                        
  

• added GUI

                   Changes in version 0.99.5                        
  

• added AnnotationHub support

                   Changes in version 0.99.4                        
  

• lazy loading to false

orthogene

                    Changes in version 1.1.5                        

BUG FIXES

• map_orthologs_babelgene
• Add “Bad credentials” check for piggyback.
• Add use_old as an optional arg so I can switch to more recent versions of babelgene::orthologs_df if need be.
• Use updated built-in babelgene::orthologs_df by default.
• Throw error if trying to map between two non-human species.
• Filter support==NA mappings by default, not but support>=2 like babelgene does by default (even when babelgene::orthologs(min_support = 1)).
• See here for discussion of discrepancies with babelgene maintainer: https://github.com/igordot/babelgene/issues/2

NEW FEATURES

• Removed aggregate_rows_delayedarray as it wasn’t being used and was far less efficient than the other methods anyway (which are also compatible with DelayedArray matrices anyway). * New unit tests:
• load_data
• aggregate_mapped_genes(method=’stat’)

• sparsity

                    Changes in version 1.1.4                        
  

BUG FIXES

• Remove source_all as it included a library call.

                    Changes in version 1.1.3                        
  

NEW FEATURES

• Update GHA

BUG FIXES

• Fix failing benchmarking tests.

                    Changes in version 1.1.2                        
  

BUG FIXES

• convert_orthologs(method=”babelgene”) now gets gene mappings from all_genes_babelgene instead babelgene::orthologs (which doesn’t seem to work very well, despite being dedicated for this purpose).
• map_species:
• Avoid running this function redundantly when nested in multiple layers of other functions.
• common_species_names_dict now return “scientific_name” by default, instead of “taxonomy_id”
• Match map_species method to whatever method is being used in the function it’s wrapped within, to avoid dropping species due to naming differences.
• Add “id” column (e.g. “celegans”) to all org databases to enhance their searchability.
• Add map_species_check_args.
• Ensure proper method-specific output_format when passing species to other functions.

NEW FEATURES

• plot_orthotree: Automated plotting of phylogenetic trees with 1:1 ortholog report annotations. Includes several subfunctions:
• prepare_tree (exported): Read, prune and standardise a phylogenetic tree.
• gather_images (internal): More robust way to find and import valid phylopic silhouettes. Will make PR requests to rphylopic and ggimage/ggtree to include this functionality.
• Added unit tests for report_orthologs, especially when method=”babelgene”.
• GitHub Actions:
• Merge both GHA workflows into one, as implemented in templateR.
• Added citation info to README.

• Save all_genes_babelgene ortholog data to orthogene-specific cache instead of tempdir to avoid re-downloading every R session.

                    Changes in version 1.1.1                        
  

BUG FIXES

• Made GHA less dependent on hard-coded R/bioc versions.

                    Changes in version 1.1.0                        
  

NEW FEATURES

• Now on Bioconductor release 3.14.
• Docker containers automatically built and pushed to DockerHub via GitHub Actions.
• Dockerfile provided to build and check any R package efficiently with AnVil.
• CRAN checks and Bioc checks run via GitHub Actions.
• Added documentation on using Docker container to README.
• Documentation website now automatically built via GitHub Actions.
• Code coverage tests now automatically run and uploaded via GitHub Actions.

PanomiR

                   Changes in version 0.99.0                        

• Submitted to Bioconductor

pareg

            Changes in version 0.99.22 (2022-02-18)                 

• Submitted to Bioconductor

pcaExplorer

                   Changes in version 2.22.0                        

Other notes

• get_annotation_orgdb() gains an additional argument, key_for_genenames, which defaults to “SYMBOL”. This should not change the behavior of the function, if not specified, but accommodates for the use of annotation packages where the information has been encoded differently (e.g. org.Sc.sgd.db where the info is contained in the “ORF” column)

Bug fixes

• pcaplot correctly returns the values for the percent of explained variance, which were correctly displayed on the plot but not stored as they should in the attribute slot

peakPantheR

             Changes in version 1.9.2 (2022-04-18)                  

• GUI corrections and improvements (use of bslib)

             Changes in version 1.9.1 (2021-12-18)                  
  

• BiocCheck format update

pengls

                    Changes in version 1.1.2                        

• Allow penalty.factor to be user supplied

                    Changes in version 1.1.1                        
  

• Also apply spatial correction to intercept

phantasus

                   Changes in version 1.15.7                        

• Using relative paths in counts metadata

                   Changes in version 1.15.5                        
  

• Fix windows-related bug in tests

                   Changes in version 1.15.3                        
  

• Major rework of RNA-seq counts support from external hdf5 files (like ARCHS4)

• Fix typing bug

                   Changes in version 1.15.1                        
  

• Option to omit gene version IDs (like in ENSEMBL) before conversion

• Annotations are trasnmitted with type information, which fixes many bugs

PhIPData

             Changes in version 1.3.3 (2022-02-04)                  

• Converted to using BiocFileCache for storing aliases and peptide libraries.

             Changes in version 1.3.2 (2022-02-02)                  
  

• Corrected typo in sample name error.

• Changed paste0() calls to file.path() calls.

PhosR

                    Changes in version 1.5.1                        

• Development version

                    Changes in version 1.4.1                        
  

• Bug fix in PCA plot variance

PhyloProfile

                    Changes in version 1.8.6                        

• option to identify sequence source

                    Changes in version 1.8.5                        
  

• added functions for exporting plot settings

                    Changes in version 1.8.4                        
  

• fixed error reading taxonNamesReduced.txt that contains “#”

• added functions for import and export taxonomy DB

                    Changes in version 1.8.3                        
  

• fixed bug of group comparison function

                    Changes in version 1.8.2                        
  

• fixed loading cluster from config file

                    Changes in version 1.8.1                        
  

• do not show pfam links for smart domains and vice versa

Pigengene

            Changes in version 1.21.40 (2022-04-15)                 

Changes in existing functions

• Habil changed the default value from hu.mouse(host=”useast.ensembl.org”, …) to hu.mouse(host=”www.ensembl.org”, …) to prevent a check error on Bioconductor.

            Changes in version 1.21.36 (2021-11-16)                 
  

Changes in existing functions

• Habil added the doReturNetworks argument to one.step.pigengene().

            Changes in version 1.21.34 (2021-11-12)                 
  

Changes in existing functions

• Habil renamed identify.modules() to determine.modules().

            Changes in version 1.21.30 (2021-11-12)                 
  

New functions

• Neda exported identify.modules(), make.filter(), and apply.filter() functions.

plotgardener

                   Changes in version 1.1.18                        

NEW FEATURES

• hicTriangles and hicRectangles can now be annotated with annoDomains or annoPixels if they are flipped.

                   Changes in version 1.1.17                        
  

NEW FEATURES

• plotIdeogram can now accept custom colors with a fill parameter. Colors can be specified with a named or unnamed vector. To see which stains are being assigned which colors, look inside the ideogram object.

                   Changes in version 1.1.16                        
  

BUG FIXES

• ENTREZ IDs obtained from AnnotationDbi::select() are subset just for ENTREZID column when determining default gene priorities, eliminating dplyr incompatible types error.

• All plus and minus strand gene name label parsing in plotGenes is now carried out only if there is a non-zero number of that strand’s genes.

                   Changes in version 1.1.15                        
  

• Citation linked for plotgardener publication in Bioinformatics.

                   Changes in version 1.1.14                        
  

BUG FIXES

• plotSignal yrange parsing for negative scores now has fixed the typo on line 418 from “score2” to “score”.

                   Changes in version 1.1.13                        
  

BUG FIXES

• plotSignal default yrange parsing now catches the invalid 0,0 range and no longer throws a viewport related error.

                   Changes in version 1.1.12                        
  

BUG FIXES

• readHic and functions related to the reading of .hic files now leaves the chromosome input formatted as is (e.g. “chr1” and “1”). Functions will throw an error if the input chromosome is not found in the chromosomes listed in the .hic file.

                   Changes in version 1.1.11                        
  

BUG FIXES

• annoDomains coordinates fixed for plotHicRectangle.
• Clipping logic for plotPairsArches now clips arches both on left and right side of plot.
• Subsetting plotPairs logic fixed to match plotPairsArches.

NEW FEATURES

• clip.noAnchors parameter in plotPairsArches allows for inclusion or clipping of arches that do not have anchors in the given genomic region.
• plotPairsArches now allows for column name input to designate archHeights.

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 1.5.16                        

• MSnbase::MSnSet class has been replaced by the SummarizedExperiment class
• Color scale for all plots set to viridis (without yellow)
• All output tables provided as tibble istead of matrix or data.frame
• Allow users to select specific covariates and their position (importance) in the model for PomaLimma, PomaUnivariate(method = “anova”), and PomaOddsRatio
• Add SD to PomaUnivariate output tables
• Reduce dependencies
• Update vignettes
• Update documentation
• Some other major and minor improvements
• Some minor bugs and typos fixed
• New “loading plot” in PCA
• Compute p-values and FDR in PomaCorr

preciseTAD

             Changes in version 1.5.0 (2022-04-21)                  

• Match NEWS and DESCRIPTION versioning

progeny

           Changes in version 2020-10-14 (2020-10-14)               

• Model matrices are not accessed in the local and not in the global enviroment

           Changes in version 2020-09-01 (2020-09-01)               
  

• Fixed issue with rownames when using Progeny with Permutations function

           Changes in version 2020-06-09 (2020-06-09)               
  

• Website: Google Analytics

           Changes in version 2020-04-27 (2020-04-27)               
  

• PROGENy website development

Major update with the following main points:

• Added the mouse model matrix containing 14 pathways

• The human model matrix extended to 14 pathways

• Added the following functions: progenyPerm, progenyScatter, progenySavePlots, getModel

• Added tests and test data

• Added the vignette for usage the PROGENy on single-cell RNA-seq data

• Added functionality to work with Seurat objects

pRolocGUI

                     Changes in version 2.5                         

CHANGES IN VERSION 2.5.4

• Fixed issue #108 by removing scrollX known issue in DT package

CHANGES IN VERSION 2.5.3

• Update README

CHANGES IN VERSION 2.5.2

CHANGES IN VERSION 2.5.1

• fix #109 bug in pRolocVis when ‘markers’ is missing from fvarLabels
• fontawesome deprecated switch to cogs for sidebar
• fix bug in colour menu #110 attributed from shinyWidgets changing the class name from checkboxGroupButtons to checkbox-group-buttons

CHANGES IN VERSION 2.5.0

• New version for Bioc

ProteoDisco

                    Changes in version 1.1.3                        

• Added citation to manuscript.

protGear

            Changes in version 0.99.546 (2022-03-25)                

• Updated the shiny app path

• Added Bioconductor installation in the app

            Changes in version 0.99.545 (2022-03-23)                
  

• Updated the NEWS file

• Removed other non Bioconductor files

            Changes in version 0.99.544 (2022-03-17)                
  

• Removed non Bioconductor files
• Added Suggests in Description
• Updated R requirement to 4.2

• Added the data documentation

            Changes in version 0.99.543 (2022-02-14)                
  

• Submitted to Bioconductor for review

            Changes in version 0.99.55 (2022-04-08)                 
  

• removed vignette.R and csv file

             Changes in version 0.99.1 (2021-12-15)                 
  

• Submitted to Bioconductor

ProtGenerics

                   Changes in version 1.27.1                        

• Add addProcessing generic <2022-01-04 Tue>

• Add new adjacencyMatrix generic <2021-12-11 Sat>

                   Changes in version 1.27.0                        
  

• New Bioc devel version

psichomics

                   Changes in version 1.20.2                        

• Bug fix: fix limma-trend approach when using newer versions of limma to calculate average gene expression

                   Changes in version 1.20.1                        
  

• Bug fix: allow to perform correlation analysis after being performed once

PSMatch

                    Changes in version 0.99                         

Changes in 0.99.5

• Fix mz calculation in calculateFragments for neutral losses with a charge > 1 (ported from MSnbase - see issue 573).

Changes in 0.99.4

• Set seed in the ConnectedComponents unit test to stop random errors after clustering.

Changes in 0.99.3

• Fix bug in describePeptides() (close #11).

Changes in 0.99.2

• Describe the ConnectedComponents() return value.
• Add/update installation instructions.

Changes in 0.99.1

• Fix typo and improve documentation.

Changes in 0.99.0

• Prepare package for Bioconductor submission.

PureCN

                    Changes in version 2.2.0                        

NEW FEATURES

• Added chunks parameter to Coverage.R and calculateBamCoverageByInterval to reduce memory usage (#218)

SIGNIFICANT USER-VISIBLE CHANGES

• When base quality scores are found in the VCF, they are now used to calculate the minimum number of supporting reads (instead of assuming a default BQ of 30). By default BQ is capped at 50 and variants below 25 are ignored. Set min.supporting.reads to 0 to turn this off (#206).

• More robust annotation of intervals with gene symbols

• Remove chromosomes not present in the centromeres GRanges object; useful to remove altcontigs somehow present (should not happen with intervals generated by IntervalFile.R)

BUGFIXES

• Fixed an issue with old R versions where factors were not converted to strings, resulting in numbers instead of gene symbols

• Fix for a crash when there are no off-target reads in off-target regions (#209).

• Fixed parsing of base quality scores in Mutect 2.2

• Fixed crash in GenomicsDB parsing when there were no variants in contig (#225)

QDNAseq

             Changes in version 1.31.0 (2021-10-27)                 

RELEASE

• The version number was bumped for the Bioconductor release version, which is now BioC 3.15 for R-devel.

QFeatures

                     Changes in version 1.5                         

QFeatures 1.5.2

• fix: implemented an updateObject() method for QFeatures objects.

QFeatures 1.5.1

• Document the use of peptide/protein adjacency matrices in aggregateFeatures() and new adjacencyMatrix() accessor.

QFeatures 1.5.0

• New devel version (Bioc 3.15)

qmtools

             Changes in version 0.99.3 (2022-04-12)                 

• The package has been accepted

• Updated the installation instruction in the README.md

             Changes in version 0.99.2 (2022-04-11)                 
  

• Updated the package documents to respond to the 2nd round of Bioconductor review

             Changes in version 0.99.1 (2022-03-17)                 
  

• Renamed the package as “qmtools”

• Made the significant changes overall according to the Bioconductor review

• Added the removeFeatures function to filter uninformative features from the data

• Added the clusterFeatures function to identify a group of features from the same originating compound

             Changes in version 0.99.0 (2022-01-03)                 
  

• Submitted to Bioconductor (The package was previously named as “poplin”)

qpgraph

                    Changes in version 2.30                         

BUG FIXES

• Fixed NAMESPACE issues

• Fixed calls to some Fortran LAPACK functions to comply with Writing R Extensions §6.6.1

qPLEXanalyzer

                   Changes in version 1.13.2                        

• Fixed guide = FALSE to guide = “none”.

                   Changes in version 1.13.1                        
  

• Fixed bug in computeDiffStats.

qsea

                   Changes in version 1.21.2                        

• increased upper bound for enrichment model, allowing for a steeper increase in enrichment with CpG density. (Github PR #9)

                   Changes in version 1.21.1                        
  

• Bugfixes:

  • makeTable with one window (github PR #8)

qsvaR

                   Changes in version 0.99.0                        

NEW FEATURES

• This is the initial version of the second iteration of the qSVA framework, which was initially described by Jaffe et al, PNAS, 2017 https://doi.org/10.1073/pnas.1617384114.

Qtlizer

             Changes in version 1.8.1 (2022-02-28)                  

• Citation adapted

RAREsim

              Changes in version 0.99.4

• Fixed format of afs_afr and nvariant_afr data

              Changes in version 0.99.3
  

• Fixed “Installing the Package” in the vignette

              Changes in version 0.99.2
  

• Reformatted vignette

• Addressed BiocCheck notes

              Changes in version 0.99.0
  

• Submitted to Bioconductor

rawrr

              Changes in version 1.3 (2022-03-19)                   

• Add barebone mode para in readSpectrum #43.

• Add rawrr namespace in help pages.

• Add ‘Monoisotopic M/Z:’ from TrailerExtraHeaderInformation as column to rawrr::readIndex function.

Rbwa

                    Changes in version 1.0.0                        

• New package Rbwa, R wrapper for BWA aligner

RcisTarget

                    Changes in version 1.15                         

• New function: showLogo() shows the motif enrichment table as HTML.

• Fix for maxRank checks: Now takes into account number of genes/regions in the database.

RCM

                   Changes in version 1.11.3                        

• For the unconstrained models: fit feature models one by one and Gram-Schmidt orthogonalize and center afterwards, rather than using Lagrange multipliers and huge Jacobian matrices. This will use less memory and speed up computations, but may yield slightly different solutions. Nothing changes for the constrained models.

                   Changes in version 1.11.2                        
  

• Explicitly import stats::model.matrix, and only load necessary VGAM functions

                   Changes in version 1.11.0                        
  

• Added FAQ section in vignette with first frequent question on number of samples not shown.
• Fixed bugs for plots of data with missing values, and added tests.

Rcpi

             Changes in version 1.31.1 (2022-04-25)                 

Improvements

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

RCy3

                   Changes in version 2.16.0                        

• Faster selectAll* functions

• Add a new vignette about cloud notebooks with RCy3

• Doc fixes:
  • Conflicting Brightness/Contrast documentation, #172
  • Conflicting Opacity documentation, #173
  • updateAnnotationText cleanup, #177
• New functions:
  • createView
  • selectAll
• Bug fixes:
  • addAnnotationShape customShape can only add rectangle, #160
  • setEdgeLineWidthMapping issue, #164
  • openAppStore function opens the Cytoscape App Store 404 web page, #169
  • groupAnnotation cleanup, #175

ReactomeGSA

             Changes in version 1.9.1 (2021-11-05)                  

• Adapted default FDR threshold in “plot_heatmap” to match other functions.

recountmethylation

                    Changes in version 1.5.1                        

• Adds QC functions for BeadArray metrics and log M/U signals

• Adds data and accessor function for cross-reactive CpGs

• Adds vignette showing how to do power analysis with pwrEWAS

• Adds vignette showing how to infer genetic ancestry using GLINT/EPISTRUCTURE

• Adds vignette showing how to do nearest neighbors search using a search index

• Adds functions for feature hashing, search index construction, and KNN search

RedeR

                    Changes in version 2.0.0                        

• Major upgrade of the user interface.

rgoslin

                    Changes in version 0.99                         

Please note that this Bioconductor version is based on Goslin version 2.0.0. See the Goslin repository for more details.

Changes in 0.99.1

• The column names within the data frames returned from the parse* methods now use column names with dots instead of spaces. This makes it easier to use the column names unquoted within other R expressions.
• All parse* methods now return data frames.
• The Messages column has been added to capture parser messages. If parsing succeeds, this will contain NA and Normalized.Name will contain the normalized lipid shorthand name.
• Parser implementations have been updated to reflect the latest lipid shorthand nomenclature changes. Please see the Goslin repository for more details.
• Exceptions in the C++ part of the library are captured as warnings in R. However, if you parse multiple lipid names, exceptions will not stop the parsing process.

rgsepd

                    Changes in version 1.27                         

• library(hash) is going away in 2022, so we need to replace that functionality with native R 4.2 environments. Shouldn’t impact users.

rhdf5

                   Changes in version 2.40.0                        

NEW FEATURES

• Added H5R functions for working with object and dataset region references.

• The HDF5 N-Bit filter has been enabled with via the function H5Pset_nbit(). This can be combined with H5Tset_precision() to compress integer and floating-point datasets.

CHANGES

• Argument ‘cset’ to h5createAttribute() and h5writeAttribute() have been deprecated. The ‘encoding’ argument should be used going forward. This ensures consistency with h5create() and h5write().

BUG FIXES

• The documentation for the ‘encoding’ argument to h5createDataset() and h5writeDataset() stated ‘UTF-8’ was a valid option, however this would produce an error. This has now been fixed. (Thanks to @ilia-kats for identifying this, https://github.com/grimbough/rhdf5/pull/101)

• Fixed bug where an uninitialized value was used in the C code underlying h5dump() potentially causing crashes.

• Addressed issue in h5dump() and h5ls() that falsely declared there were duplicated groups when used on a file with external links (Thanks to @acope3 for reporting this, https://github.com/grimbough/rhdf5/issues/107).

Rhdf5lib

                    Changes in version 1.18                         

New features

• Package now includes precompiled libraries for Windows built with the UCRT toolchain for R-4.2

• Swap bundled version of SZIP for LIBAEC. This now reflects the official HDF5 group releases.

• The HDF5 configure option “–disable-sharedlib-rpath” is now exposed during package installation (thanks to Ben Fulton @benfulton, https://github.com/grimbough/Rhdf5lib/pull/39)

Rhtslib

                   Changes in version 1.28.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Acknowledge site-wide or user-specified Makevars file if present.

RiboDiPA

                    Changes in version 1.3.1                        

• Functions to visualize tracks through genome browser igvr added

• Functions to export ribo-seq tracks to external genome browser added

ribosomeProfilingQC

                    Changes in version 1.7.1                        

• export readLen for estimatePsite.

RMassBank

                    Changes in version 3.5.1                        

• Switch to using mzML files in the vignette after mzR dropped support for mzData

RnaSeqSampleSize

             Changes in version 2.5.1 (2021-12-02)                  

NEW FEATURES

• Support defining ratio of sample size between two groups by parameter k

BUG FIXES

• Change website URL in vignette

• Not-Run some example codes

RnBeads

                   Changes in version 2.13.2                        

• Removed support for RefFreeEWAS, since the package is not supported anymore

RolDE

                   Changes in version 0.99.4                        

• Updated version dependency to R to 4.2.0.

                   Changes in version 0.99.3                        
  

• Added Bioconductor installation instructions in the Vignette.

• Fixed some bugs related to changing coding practices in v. 0.99.2

                   Changes in version 0.99.2                        
  

• Added a NEWS file.

• Added Bioconductor installation instructions in README.

• Removed separate licence file. Using GPL-3 licence.

• Added information for the included datasets.

• Added table of contents for the vignette.

• Updated the RolDE main functions documentation.

• Improved coding practices to match more Bioconductor style.

                   Changes in version 0.99.1                        
  

• Submitted to Bioconductor.

rols

                    Changes in version 2.23                         

CHANGES IN VERSION 2.23.2

• Remove failing CVParams() examples

CHANGES IN VERSION 2.23.1

• Don’t show empty termDesc(trm) in vignette.

CHANGES IN VERSION 2.23.0

• New devel version

ropls

                   Changes in version 1.27.8                        

MINOR MODIFICATION

• minor vignette correction

                   Changes in version 1.27.6                        
  

MINOR MODIFICATION

• minor vignette correction

                   Changes in version 1.27.4                        
  

MINOR MODIFICATION

• minor vignette update

                   Changes in version 1.27.2                        
  

MINOR MODIFICATION

• minor documentation update

rpx

                    Changes in version 2.3.0                        

rpx 2.3.3

• Don’t run caching example as it replies on PRIDE which is failing too often for the tests to pass on all systems.

rpx 2.3.2

• Provide fix for PRIDE migration and annotation discrepancies (see issue #17). This fix will however lead to re-downloading some cached files due to different URLs. The fix might only be temporary, based on if/how PRIDE will address their inconsistencies.

rpx 2.3.1

• Use BiocFileCache::bfcrpath to get correct rpath, irrespective of absolute or relative.

rpx 2.3.0

• New bioconductor devel branch

rrvgo

                    Changes in version 1.7.1                        

• Deprecate org.Pf.plasmo.db

Rsubread

                   Changes in version 2.10.0                        

• Added inbuilt RefSeq annotation for mm39 (mouse genome Build 39).

• Streamlined the mapping and counting processes in cellCounts.

• Added support for processing dual-index 10x data in cellCounts.

rWikiPathways

                   Changes in version 1.16.0                        

• HTTPS updates

• Update vignette to include new clusterProfiler functions

S4Vectors

                   Changes in version 0.34.0                        

NEW FEATURES

• Implement subassignment of TransposedDataFrame objects.

SIGNIFICANT USER-VISIBLE CHANGES

• DataFrame is now a virtual class! This completes the replacement of DataFrame with DFrame announced in September 2019. See: https://www.bioconductor.org/help/course-materials/2019/BiocDevelForum/02-DataFrame.pdf

BUG FIXES

• Avoid spurious warnings when DataFrame() is supplied a DataFrameList.

• Fix bug in combineRows(DataFrame(), DataFrame(ref=IRanges(1:2, 10))).

• Fix display of TransposedDataFrame objects with more than 11 rows.

• Fix isEmpty() on ordinary lists and derivatives.

• Fix handling of nested DataFrames in combineUniqueCols().

• Make sure internal helper lowestListElementClass() does not lose the “package” attribute of the returned class (fixes issue #103).

satuRn

                    Changes in version 1.3.1                        

• Bug fix: allow for fit errors to be propagated as NA results (github issue 15 by @jgilis)
• Bug fix: handle experimental designs with empty factor levels correctly (github issue 16 by @XueyiDong)
• Bug fix: identify transcripts that are the only expressed transcript of a gene and set NA results (github issue 17 by @jgilis)
• Bug fix: handle extreme z-scores in testDTU with diagplot2 option
• Enhancement: plotDTU now allows for sparseMatrix input

SCArray

                    Changes in version 1.4.0                        

• new functions scMEX2GDS() and scHDF2GDS()

                    Changes in version 1.2.1                        
  

• new Overview.Rmd in the vignettes

scater

                   Changes in version 1.24.0                        

• Remove diffusion map functions that relied on destiny.

• Add point.padding,force args to plotReducedDim; passed to geom_text_repel.

• Add warning about unused use_dimred argument in runTSNE.

scDblFinder

             Changes in version 1.9.11 (2022-04-16)                 

• fixed larger kNN size

                    Changes in version 1.9.9                        
  

• improved amulet reimplementation

• added clamulet and scATAC vignette

             Changes in version 1.9.1 (2021-11-02)                  
  

• added reimplementation of the amulet method for scATAC-seq

scPCA

             Changes in version 1.9.1 (2022-01-19)                  

• Updating copyright years
• Updating citation information

scTensor

                    Changes in version 2.4.1                        

• A vignette modified.

sechm

             Changes in version 1.3.1 (2022-04-15)                  

• fixed a few bugs

• better support for default arguments

• removed deprecated arguments

• added meltSE

seqArchR

                  Changes in version 0.99.339                       

• seqArchR available on Bioconductor

                   Changes in version 0.99.0                        
  

New features

• viz_seqs_acgt_mat() function can now add a legend via new arguments add_legend and use_legend.
• Package name change from archR to seqArchR

Breaking changes

• (User-facing) Function name archR_set_config() changed to set_config()
• (User-facing) Function name viz_seqs_acgt_mat_from_seqs() changed to viz_seqs_acgt_mat()
• (User-facing) Function runArchRUI() that launched a Shiny app is moved to a different package coming up in the future

SeqArray

                   Changes in version 1.36.0                        

NEW FEATURES

• new functions seqUnitCreate(), seqUnitSubset() and seqUnitMerge()

• new functions seqFilterPush() and seqFilterPop()

• new functions seqGet2bGeno() and seqGetAF_AC_Missing()

• new function seqGetData(, "$dosage_sp") for a sparse matrix of dosages

• the first argument ‘gdsfile’ can be a file name in seqAlleleFreq(), seqAlleleCount(), seqMissing()

• new function seqMulticoreSetup() for setting a multicore cluster according to a numeric value assigned to the argument ‘parallel’

UTILITIES

• allow opening a duplicated GDS file (‘allow.duplicate=TRUE’) when the input is a file name instead of a GDS object in seqGDS2VCF(), seqGDS2SNP(), seqGDS2BED(), seqVCF2GDS(), seqSummary(), seqCheck() and seqMerge()

• remove the deprecated ‘.progress’ in seqMissing(), seqAlleleCount() and seqAlleleFreq()

• add summary.SeqUnitListClass()

• no genotype and phase data nodes from seqSNP2GDS() if SNP dosage GDS is the input

BUG FIXES

• seqUnitApply() works correctly with selected samples if ‘parallel’ is a non-fork cluster

• seqVCF2GDS() and seqVCF_Header() work correctly if the VCF header has white space

• seqGDS2BED() with selected samples for sex and phenotype information

• buf fix in seqGDS2VCF() if there is no integer genotype

seqcombo

                   Changes in version 1.17.1                        

• update docs (2021-12-15, Wed)
• remove codes that were incorporated in ggmsa

SEtools

             Changes in version 1.9.2 (2022-04-16)                  

• removed functions that have been moved to the sechm package

signatureSearch

             Changes in version 1.9.6 (2022-01-28)                  

• Addressed warning for non-ascii in cell_info2

             Changes in version 1.9.5 (2022-01-26)                  
  

• Updated lincs_pert_info2 and cell_info2

             Changes in version 1.9.3 (2021-12-17)                  
  

• Supported searching against the newest LINCS 2020 beta database in devel version

• Modified gess_* functions to support adding customized compound annotation table to the GESS result table.

             Changes in version 1.9.2 (2021-12-06)                  
  

• Move eh to .onLoad function

simplifyEnrichment

                    Changes in version 1.5.2                        

• add keyword_enrichment_from_GO()

                    Changes in version 1.5.1                        
  

• word cloud supports perform enrichment on keywords

• value_fun in binary_cut() now takes 1-AUC as default

singleCellTK

                    Changes in version 2.5.2                        

• Added Seurat report functions
• Added TSCAN trajectory analysis functions
• Refactored EnrichR wrapper function (runEnrichR)
• Added new cut-offs for DE functions

• Other refactors and bug fixes

             Changes in version 2.5.1 (2022-03-31)                  
  

• Added SoupX method for decontamination (runSoupX)
• Added useReducedDim parameter for DE analysis and Heatmap
• Added Differential Abundance section to the tutorials
• Fixed Mitochondrial gene list

• Other refactors and bug fixes

             Changes in version 2.4.1 (2021-12-22)                  
  

• Added new function for DEG volcano plot (plotDEGVolcano)
• Added new function for plotting pathway scores (plotPathway)
• Added Pathway Analysis section to the tutorials
• Added seed parameter to several functions and UI for reproducibility
• Updated R console and GUI tutorials to match each other
• Fixed console logging in the GUI

sitePath

                   Changes in version 1.11.2                        

• More function availability for objects

                   Changes in version 1.11.1                        
  

• Wrapper function for finding fixation and parallel sites

• Core number set to 1 will disable multiprocessing

SNPRelate

                   Changes in version 1.30.0                        

• return a object of S3 class “snpgdsGRMClass” in snpgdsGRM() instead of a list when with.id=TRUE

sparrow

                     Changes in version 1.2                         

Enhancements

• The default “zero-centering” logic is updated in mgheatmap2 when col isn’t specified, but recenter is (backported to release 3.14)

Bug Fixes

• calculateIndividualLogFC is updated to handle situations when $genes data.frame has column names that collide with statistics generated from differential expression, like pval, padg, and AveExpr. Thanks to @sandersen12 for the bug report.

SpatialDecon

             Changes in version 1.5.0 (2021-10-27)                  

• No changes from 1.3.0

SpatialExperiment

             Changes in version 1.5.3 (2022-02-28)                  

• rename SpatialImage class to VirtualSpatialImage

             Changes in version 1.5.2 (2022-01-09)                  
  

• relocate and deprecate spatialData/Names

             Changes in version 1.5.1 (2021-12-15)                  
  

• improved coercion methods from SingleCellExperiment to SpatialExperiment

• add new methods for image rotation/mirroring

• add path argument to imgSource()

• user flexibility whether to provide outs/ directory in read10xVisium()

• documentation updates in show methods

• additional documentation updates

• update title and description in DESCRIPTION

spatialHeatmap

             Changes in version 2.1.1 (2022-04-06)                  

• Developed the new functionality co-visualization of bulk and single cell data through auto-matching/coclustering, i.e. source bulk tissues are matched/assigned to single cells automatically through coclustering. This feature is implemented in both command line and Shiny app with testing data provided.

• Developed optimization functions for coclustering workflow with testing data provided.

• Co-visualization through manual matching was implemented in command line.

spatzie

                    Changes in version 1.0.1                        

• added reference to NAR paper

Spectra

                     Changes in version 1.5                         

Changes in 1.5.20

• Add parameters ppm and tolerance to PrecursorMzParam (for neutral loss calculation) and add option filterPeaks = “removePrecursor”.

Changes in 1.5.19

• Improved the bin method.

Changes in 1.5.18

• Set default for parameter columns in peaksData,Spectra and peaksData,MsBackend to c(“mz”, “intensity”).

Changes in 1.5.17

• Add peaksVariables method and add parameter columns (or …) to peaksData.
• Add columns parameter to the peaksData method of MsBackendDataFrame, MsBackendMzR and MsBackendHdf5peaks.

Changes in 1.5.16

• Fix issue in neutralLoss that would prevent calculation of neutral loss spectra if

Changes in 1.5.15

• Fix typo in MZ delta plot title.

Changes in 1.5.14

• Add coreSpectraVariables function to export the core spectra variables and their expected data types.

Changes in 1.5.13

• Fix figure sizes in vignette.

Changes in 1.5.12

• Add neutralLoss method and first algorithm to calculate neutral loss spectra.

Changes in 1.5.11

• Fix neutral loss example in the vignette.

Changes in 1.5.10

• Add citation.

Changes in 1.5.9

• Add examples for combineSpectra to the vignette.

Changes in 1.5.8

• Add spectraVariableMapping generic.

Changes in 1.5.7

• Add missing export of the filterPrecursorMz method.

Changes in 1.5.6

• Add filterPrecursorMzValue method which allows to filter using multiple precursor m/z values (issue #230).
• Fix unit test suite.

Changes in 1.5.5

• Add a testing framework allowing to run standardized unit tests for new MsBackend implementations (issue #186).

Changes in 1.5.4

• Add the MsBackendCached backend.

Changes in 1.5.3

• Only calculate number of peaks per spectra if the processing queue of the Spectra is not empty. Otherwise call the backend’s implementation (issue MsBackendSql #31).

Changes in 1.5.2

• Small documentation update (related to MsCoreUtils issue #87).
• New countIdentifications() function.
• Add filterFourierTransformArtefacts function to remove fast fourier artefact peaks seen on e.g. Orbitrap instruments (issue #223).

Changes in 1.5.1

• Don’t read header information when importing peaks matrix on macOS.

SpectralTAD

             Changes in version 1.11.0 (2022-04-21)                 

• Match NEWS and DESCRIPTION versioning

splatter

             Changes in version 1.20.0 (2022-04-27)                 

• The splatPop simulation is now published doi.org/10.1186/s13059-021-02546-1!

• Improved initalisation of Params objects (from Wenjie Wang)

• Improved fitting of dropout in splatEstimate()

• Better initialisation of fitting as suggested by the InferCNV package

• Additional fallback method

• Bug fixes for the splat simulation

• Bug fixes for the the splatPop simulation (from Christina Azodi)

SplicingFactory

                    Changes in version 1.3.1                        

• Citation update
• Other minor corrections

SPOTlight

                   Changes in version 0.99.1                        

• text

                   Changes in version 0.99.0                        
  

• initial submission to Bioc devel v3.15

sSNAPPY

                   Changes in version 0.99.1

• Updated vignette to use pre-computed output

• Allow removal of isolated nodes in plot_gs_network

                   Changes in version 0.99.0                        
  

• Submitted to Bioconductor

standR

                   Changes in version 0.99.0                        

• First release of the package.

statTarget

                   Changes in version 1.25.4                        

• Remove the RGtk2 in Description, which should be installed manually from the old source

                   Changes in version 1.24.1                        
  

• Remove the GUI

STdeconvolve

                    Changes in version 0.99.10

• R version for Bioconductor and package branch: (>= 4.1)

• R version in devel branch in GitHub: (>= 3.6)

                    Changes in version 0.99.0
  

• Submitted to Bioconductor

struct

                    Changes in version 1.7.1                        

• fix as.code generic

• improve as.code for all objects

structToolbox

                    Changes in version 1.7.2                        

• internal updates to PLS

• some PLS charts have been renamed for consistency with other methods

                    Changes in version 1.6.1                        
  

• hotfix vector_norm now correctly normalises samples to length 1

• added vector_norm_tests

SummarizedExperiment

                   Changes in version 1.26.0                        

DEPRECATED AND DEFUNCT

• readKallisto() is now defunct after being deprecated in BioC 3.12.

SynExtend

                   Changes in version 1.7.14                        

• Various improvements for GenRearrScen, improves consistency and output formatting
• Major bugfix for ProtWeaver methods using dendrogram objects

• ProtWeaver now correctly guards against non-bifurcating dendrograms in methods that expect it

                   Changes in version 1.7.13                        
  

• Introduces new ProtWeaver class to predict functional association of genes from COGs or gene trees. This implements many algorithms commonly used in the literature, such as MirrorTree and Inverse Potts Models.
• predict(ProtWeaverObject) returns a ProtWeb class with information on predicted associations.

• Adds BlastSeqs to run BLAST queries on sequences stored as an XStringSet or FASTA file.

                   Changes in version 1.7.12                        
  

• Updates to ExtractBy function. Methods and inputs simplified and adjusted, and significant improvements to speed.

                   Changes in version 1.7.11                        
  

• Updated NucleotideOverlaps to now correctly registers hits in genes with a large degree of overlap with the immediately preceding gene.

• Fixed aberrant behavior in BlockExpansion where contigs with zero features could cause an error in expansion attempts.

                   Changes in version 1.7.10                        
  

• BlockReconciliation now allows for setting either block size or mean PID for reconciliation precedence.

                    Changes in version 1.7.9                        
  

• Added retention thresholds to BlockReconciliation.

                    Changes in version 1.7.8                        
  

• BlockExpansion cases corrected for zero added rows.

                    Changes in version 1.7.7                        
  

• Improvements to BlockExpansion and BlockReconciliation functions.

                    Changes in version 1.7.5                        
  

• Began integration of DECIPHER’s ScoreAlignment function.

                    Changes in version 1.7.4                        
  

• Fixed a bug in PairSummaries function.

                    Changes in version 1.7.3                        
  

• Added BlockExpansion function.

                    Changes in version 1.7.2                        
  

• Adjustment in how PairSummaries handles default translation tables and GFF derived gene calls.

                    Changes in version 1.7.1                        
  

• Large changes under the hood to PairSummaries.
• Failure to accurately assign neighbors in some cases should now be fixed.
• Extraction of genomic features is now faster.
• OffSetsAllowed argument now defaults to FALSE. This argument may be dropped in the future in favor of a more complex function post-summary.
• Small edits to SequenceSimilarity

systemPipeShiny

                   Changes in version 1.5.10                        

Major Change

• Redesign of the welcome page. Old content is moved to about. Now the welcome page is more clear.

• Adapt SPR to the 2.1.x version.

• Add more instructing images to the workflow module.
• A warning message is added if spsOption(“demo”, TRUE), to let people know some workflow templates will fail if they use the demo server to run jobs.

Minor Change

• Fix some text typo, links.
• Add more figures as instructions in different modules/tabs.
• Text/links fixed in workflow module.

TADCompare

             Changes in version 1.5.0 (2022-04-21)                  

• Match NEWS and DESCRIPTION versioning

TargetSearch

                   Changes in version 1.52.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Deprecate parameter ‘libId’ and replace it with ‘libID’ The parameter libId conflicts with the method libId, and in other functions we already use a variable libID that correspond with the library identifier. Therefore, we replace it for consistency. This change affects the functions plotRIdev, plotSpectra and

BUG FIXES

• plotRIdev: use near equality for comparison. The function compares the selective or top masses against the columns of the intensity matrix. However, their lengths are variable, so the for if condition threw a warning if the lengths didn’t match.

• Refactor functions binsearch and find_peaks. Minor optimization to the function binsearch in which the starting RT scan is found directly. This will reduce a couple of CPU cycles.

• Extra CDF integrity checks. Check that the length of the variables are all greater than zero and replace logical OR operator for its longer form.

                   Changes in version 1.50.1                        
  

BUG FIXES

• Fixes the gcc warning produced by passing a pointer and with an incorrect size to the function swapb. This went undiscovered for years because the code is only executed in big-endian machines.

TBSignatureProfiler

                    Changes in version 1.7.1                        

Bug Fixes

• Fixed gene in RESPONSE5 (PNN to RP11-295G20.2) in TBsignatures and TBcommon objects. (Stanley M. Kimbung)

Major Changes

• If any signatures in the object used with runTBsigProfiler() have <2 genes present in the given sample, the signatures will not be scored. This may affect existing scripts.
• Fixed a bug in the singscore algorithm called from runTBsigProfiler() that would not allow for the scoring of user-provided signatures.

Minor Changes

• Reorganized code for OriginalModel.R for clarity.
• Fixed the TB_hiv data to remove unnecessary factor level of Disease metadata.
• Added 4 new signatures (Tabone_OD_11/TB12, Tabone_RES_25/EarlyRESP-TB25, Tabone_RES_27/TREAT-TB27, Long_RES_10)
• Updated the website interface
• Changed HGNChelper installation to be checked during profiling if update_genes = TRUE
• Reorganized code in mkAssay() for clarity. The output_name argument is now appended to all output assays, whereas previously it was only appended to the log of the input assay.
• Fixed the row numbers of existing sigAnnotData and common_sigAnnotData objects, and added code to update them after new signatures are added.

TCGAutils

                   Changes in version 1.16.0                        

New features

• The UUIDhistory function allows users to map old UUIDs to new UUIDs according to the latest data release for UUIDs that were affected and no longer query-able.
• The slides argument has been added to the filenameToBarcode function for translating slide file names into barcodes. Currently, the API returns all barcodes of the associated case ID.
• Add sections in the vignette regarding GDC Data Updates and UUID history lookup

Minor changes and bug fixes

• Update examples in package to new GDC Data Release, see vignette.
• Use AnnotationHub to download chain file in main vignette.
• Slide file names now resolve to a single TCGA barcode in filenameToBarcode (Thanks @hermidalc)
• Improved error messages and documentation for makeGRangesListFromExonFiles

TFEA.ChIP

                   Changes in version 1.15.2                        

New ChIP-Gene databases available

• Using ReMap2022 collections for human and mouse.

• Adding cell specific regulatory regions predicted with ABC-Enhancer-Gene-Prediction (doi:10.1038/s41588-019-0538-0).

New Features

• New database format (older databases are still compatible). The format consist of a list containing two elements:
  • Gene Keys: vector of gene IDs
  • ChIP Targets: list of vectors, one per ChIP-seq experiment, containing the putative targets assigned. Each target is coded as its position in the vector ‘Gene Keys’.
• Database generation has been streamlined by joining together the functions GR2tfbs_db() and makeTFBSmatrix() into one, makeChIPGeneDB().

New default database

• The TF-Gene database included with TFEA.ChIP was built using ReMap’s ChIP-seq collection (v. 2022) and GeneHancer’s Double Elite regulatory regions (v. 4.8). Because of memory limits, the internal database included in TFEA.ChIP can only store a fraction of the 8000+ ChIP-seq experiments in the colection. We selected the 926 ChIP-seq experiments done in ENCODE Project’s Common Cell Types. To download the full database, as well as other ready-to-use databases generated for TFEA.ChIP, visit: https://github.com/LauraPS1/TFEA.ChIP_downloads

tomoda

                    Changes in version 1.5.0                        

• Fixed bug in normalizeTomo()

tomoseqr

             Changes in version 0.99.0 (2022-03-28)                 

• Submitted to Bioconductor

topdownr

                    Changes in version 1.17                         

Changes in version 1.17.3

• Depending on mzR 2.27.5.
• Fix unit test for .readSpectrum to adapt to new mzR 2.27.5.

Changes in version 1.17.2

• Fix roxygen2 warnings.

Changes in version 1.17.1

• New version for Bioc 3.15 (devel)
• Adapt to new DFrame.

trackViewer

                   Changes in version 1.31.4                        

• Fix the issue in windows 2022.

                   Changes in version 1.31.2                        
  

• Handle the issue with long tail.

                   Changes in version 1.31.1                        
  

• Move the heatmap legend to yaxis.

transformGamPoi

                     Changes in version 1.1                         

• Implement faster scaling with size factors for acosh and log-based transformations
• Implement analytic Pearson residuals

transite

                   Changes in version 1.12.1                        

• Fix typos

treeio

                   Changes in version 1.19.2                        

• update offspring() to work as child(). Actually they are using the same function with different default (child(type = “children”) and offspring(type=”all”)) (2022-03-16, Wed)
• update child() to support different types (“children”, ‘tips’, ‘internal’, ‘external’, ‘all’) (2022-03-09, Wed, #75)

• write.beast allows treedata object only contains phylo slot, then it will equivalent to write.nexus (2022-02-23, Wed)

                   Changes in version 1.19.1                        
  

• bug fixed in groupClade.treedata to return a treedata object instead of phylo (2021-11-12, Fri)

TREG

                   Changes in version 0.99.0                        

NEW FEATURES

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

SIGNIFICANT USER-VISIBLE CHANGES

• Your main changes to a function foo() or parameter param.

BUG FIXES

• Your bug fixes. See more details at http://bioconductor.org/developers/package-guidelines/#news.

tricycle

                    Changes in version 1.3.4                        

• Update tricycle citation.

tximeta

                   Changes in version 1.14.0                        

• Allow GTF specification in linkedTxome to be a serialized GRanges file (a file path to a .rda or .RData file). This bypasses some apparent issue where makeTxDbFromGFF fails while makeTxDbFromGRanges works.

• Up to GENCODE 40 (H.s.), M29 (M.m), and Ensembl 106

UCell

                    Changes in version 2.0.0                        

• Update code to pass all BioC checks.

• The function ScoreSignatures_UCell() and StoreRankings_UCell() accept directly sce objects.

• Takes custom BiocParallel::bpparam() object as input to specify parallelisation.

                    Changes in version 1.3.1                        
  

• Restructure code to conform to BioC standards.

• Switch from future to BiocParallel to parallelize jobs.

• Add support for SingleCellExperiment - new function ScoreSignatures_UCell_sce() interacts directly with sce objects.

• Signatures cannot be larger than maxRank parameter.

• Do not rank more genes (maxRank) than there are in the input matrix.

universalmotif

                   Changes in version 1.14.0                        

NEW FEATURES

• enrich_motifs(mode, pseudocount): Choose whether to count motif hits once per sequence, and whether to add a pseudocount for P-value calculation.

• New function, meme_alph(): Create MEME custom alphabet definition files.

• merge_similar(return.clusters): Return the clusters without merging.

• convert_motifs(): MotifDb-MotifList now available as an output format.

MINOR CHANGES

• enrich_motifs(): RC argument now defaults to TRUE, increased max significance values, no.overlaps now defaults to TRUE. Additional columns showing the motif consensus sequence and percent of sequences with hits are now included.

• scan_sequences(RC): Only print a warning if RC=TRUE for non-DNA/RNA motifs.

• Reduced the size of the message when a pseudocount is added to motifs.

                   Changes in version 1.12.4                        
  

BUG FIXES

• convert_motifs(): Properly handle TFBSTools class motifs with ‘’ as their strand. This was achieved by making the universalmotif object creator tolerant to using ‘’ as a user input. Thanks to David Oliver for the bug report (#22).

                   Changes in version 1.12.3                        
  

BUG FIXES

• scan_sequences(): Previously this function did not account for the fact that duplicate sequence names are allowed within XStringSet objects. To better keep track of which sequence hits are associated with, an additional sequence.i column has been added which keeps track of the sequence number. This change also fixes a knock-on issue with enrich_motifs(), where sequences with duplicate names did not contribute to the count of sequences containing hits. Thanks to Alexandre Blais for mentioning this issue.

                   Changes in version 1.12.2                        
  

BUG FIXES

• shuffle_sequences(…, method=”markov”): Previously the returning sequences were longer by 1.

                   Changes in version 1.12.1                        
  

BUG FIXES

• DNA ambiguity letters can be used with create_motif() when alphabet=”DNA” is specified. Previously ambiguity letters only worked when alphabet was not specified.

updateObject

                    Changes in version 1.0.0                        

• First version of the package that is ready for general use.

variancePartition

                   Changes in version 1.25.13                       

• Fix compatibility issue with lme4 1.1.29

• reported https://github.com/GabrielHoffman/variancePartition/issues/51

                   Changes in version 1.25.12                       
  

• in makeContrastsDream(), fix issue where terms with colon cause and error

                   Changes in version 1.25.11                       
  

• fix bug in dream() for variables with NA values

• improve handling of invalid contrasts in makeContrastsDream()

                   Changes in version 1.25.9                        
  

• for getContrast() and makeContrastsDream() make sure formula argument is a formula and not a string

                   Changes in version 1.25.8                        
  

• small bug fixes

                   Changes in version 1.25.7                        
  

• dream() now drops samples with missing data gracefully

                   Changes in version 1.25.6                        
  

• fix small plotting bug in plotStratify() and plotStratifyBy()

                   Changes in version 1.25.5                        
  

• add getTreat() to evaluate treat()/topTreat() seamlessly on results of dream()

                   Changes in version 1.25.4                        
  

• in dream() set default ddf = “adaptive”, which uses “KR” for less than 12 samples
• all functions default tp BPPARAM=SerialParam()

• add eBayes() to vignette for dream()

                   Changes in version 1.25.3                        
  

• add genes argument to plotPercentBars()

                   Changes in version 1.25.2                        
  

• change plotPercentBars() to use generic S4

                   Changes in version 1.25.1                        
  

• update handling of weights in voomWithDreamWeights() and add applyQualityWeights()

VaSP

             Changes in version 1.7.2 (2022-01-07)                  

• Removed the visualizing function splicePlot due to the dependent package Sushi deprecated.

velociraptor

                    Changes in version 1.5.2                        

• Remove column names of reduced dimension representation before velocity embedding.

                    Changes in version 1.5.1                        
  

• Add example for scvelo.params argument.

vissE

                    Changes in version 1.4.0                        

• Added the adjusted rand index as a measure of gene-set overlap (now the default measure of overlap).
• Added feature to only plot gene-sets that are marked in the plotMsigNetwork function.
• Added function to identify and prioritise gene-set clusters (findMsigClusters)

weitrix

                    Changes in version 1.7.1                        

• counts_shifts and counts_proportions now have a “typecast” argument, allowing use of memory-efficient matrix types.

xcms

                   Changes in version 3.17.6                        

• Rewrite code to subset features and chromatographic peaks. This results in a perfomance improvement for filterFile and similar functions.

• Add parameter expandMz to featureChromatograms (https://github.com/sneumann/xcms/issues/612).

                   Changes in version 3.17.5                        
  

• Change the way the m/z value for a chromatographic peak is determined by centWave: if a ROI contains more than one peak for one scan (spectrum) an intensity-weighted m/z is reported for that scan. The m/z of the chromatographic peak is then calculated based on these reported m/z values for each scan (spectrum). In the original version the mean m/z for a scan was reported instead. As a result, m/z values of chromatographic peaks are now slightly different but are expected to be more accurate. See https://github.com/sneumann/xcms/issues/590 for more details.

                   Changes in version 3.17.4                        
  

• Add transformIntensity method.

• Fix issue when calling chromPeakSpectra or featureSpectra on an object that contains also files with only MS1 spectra (https://github.com/sneumann/xcms/issues/603).

                   Changes in version 3.17.2                        
  

• Use mzML instead of mzData files in testing and vignettes, since mzR drop mzData reading and msdata package will drop mzData files as well

                   Changes in version 3.17.1                        
  

• Fix bug in feature grouping by EIC correlation that would return a non-symmetric similarity matrix.

• Fix error message from issue 584.

zellkonverter

                    Changes in version 1.6.0                        

Major changes

• Added support for multiple basilisk environments with different anndata versions. Users can now specify the environment to use with options in readH5AD() and writeH5AD(). To faciliate this some exported objects where converted to functions but this should only effect developers.

• Updated the default environment to use anndata v0.8.0. This is a major update and files written with v0.8.0 cannot be read by previous anndata versions. This was the motivation for supporting multiple environments and users can select the previous environment with anndata v0.7.6 if compatibility is required.

• Standardise naming in AnnData2SCE(). Column names of data frames and names of list items will now be modified to match R conventions (according to make.names()). When this happens a warning will be issued listing the modifications. This makes sure than everything in the created SingleCellExperiment is accessible.

Minor changes

• Allow data.frame’s stored in varm to be converted in SCE2AnnData()

• Minor updates to the vignette and other documentation.

• Updates to tests to match the changes above.

NEWS from new and existing Data Experiment Packages

crisprScoreData

                   Changes in version 0.99.0                        

• Package submission

curatedMetagenomicData

                    Changes in version 3.4.0                        

• curatedMetagenomicData now contains 20,533 samples from 90 studies
• A total of 251 samples added since Bioconductor 3.14 (October 2021)
• Studies added since Bioconductor 3.14 (October 2021):
• FrankelAE_2017 (39 samples)
• LeeKA_2022 (165 samples)
• PetersBA_2019 (27 samples)
• WindTT_2020 (20 samples)
• Both “short” and “NCBI” row names were re-validated against NCBI Taxonomy

depmap

                     Changes in version 1.9                         

Changes in version 1.9.2

• 22Q1 data added for crispr, copyNumber, TPM, mutationCalls and metadata datasets. New datasets were added, including gene_summaries and achilles describing Depmap Achilles screens and gene essentiality probabilities, respectively. New loading functions were created for these datasets. Newer versions for the other datasets were not released.

Changes in version 1.9.1

• 21Q4 data added for crispr, copyNumber, TPM, mutationCalls and metadata datasets. Newer versions for the other datasets were not released.

Changes in version 1.9.0

• New devel version for Bioc 3.15

Changes in version 1.7.1

• 21Q3 data added for crispr, copyNumber, TPM, mutationCalls and metadata datasets. Newer versions for the other datasets were not released.
• CERES CRISPR data has been deprecated and has been replaced with Chronos CRISPR dependency in 21Q3 and all future releases. For more information, see: https://cancerdatascience.org/blog/posts/ceres-chronos/

Changes in version 1.7.0

• New Bioc devel release.

dorothea

             Changes in version 1.7.1 (2022-04-07)                  

• Removed outdated vignettes, now instead we point to decoupleR and decoupler-py’s most up-to-date vignettes.

epimutacionsData

                   Changes in version 0.99.7                        

• Bugs and notes (if possible) fixed

                   Changes in version 0.99.0                        
  

• Submitted to Bioconductor

FlowSorted.Blood.EPIC

             Changes in version 1.99.1 (2022-01-04)                 

• Made the following significant changes o The IDOL libraries are automatically selected o The slot counts is now only for cell counts, if available o Projections are based on cell proportions o estimateCellCounts2 supports additional packages and extended deconvolution o The reference library is called using libraryDataGet

healthyControlsPresenceChecker

            Changes in version 0.99.17 (2021-11-29)                 

• Fixed YAML

            Changes in version 0.99.15 (2021-11-26)                 
  

• Fixed additional minor issues

            Changes in version 0.99.13 (2021-11-24)                 
  

• Fixed additional minor issues

            Changes in version 0.99.12 (2021-11-22)                 
  

• Fixed minor issues

            Changes in version 0.99.11 (2021-11-19)                 
  

• Added unit tests

            Changes in version 0.99.10 (2021-11-18)                 
  

• Edited vignettes

             Changes in version 0.99.9 (2021-11-18)                 
  

• Addressed points of the review and added a README

             Changes in version 0.99.1 (2021-10-29)                 
  

• First release

             Changes in version 0.1.6 (2021-11-02)                  
  

• Added print of the percentages of the elements of the healthy controls and of the other classes

msdata

                   Changes in version 0.35.3                        

• Adding CE-MS test data, thanks to Liesa Salzer

pRolocdata

                   Changes in version 1.33.1                        

• Add hyperLOPIT2015_se data

• Add mulvey2015_se and mulvey2015norm_se data

• Regenerated README to include new datasets

scpdata

                     Changes in version 1.3                         

scpdata 1.3.1

• williams2020: added 2 new datasets (need to be sent to EH)
• all: added supplementary metadata fields in metadata.csv.
• zhu2019EL: split protein data into protein_intensity and protein_iBAQ
• dou2019: modified peptide data by excluding low-quality PSMs

scpdata 1.3.0

• New devel (Bioc 3.15)

signatureSearchData

             Changes in version 1.9.3 (2021-12-16)                  

• Add LINCS2 database with file name of lincs2020.h5

             Changes in version 1.9.2 (2021-12-06)                  
  

• Add dest_path parameter to getCmapCEL function

spatialLIBD

                   Changes in version 1.7.19                        

SIGNIFICANT USER-VISIBLE CHANGES

• Documentation of the layer-level data panel at run_app() has been significantly increased. You can now also visualize more than 2 reduced dimensions computed on the pseudo-bulk level data (layer-level for the Maynard et al, Nature Neurosci, 2021 data).
• Users can now control the font and point size on the reduced dimension plots, as well as the overall font size on the model boxplots.

• Image edit scenarios you might be interested in for having a uniform color background image are now documented; for example if you want a white or black background, or actually any valid R color name or color HEX value.

                   Changes in version 1.7.18                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• run_app() now offers the option to chose any of the paletteer::paletteer_d color palettes for discrete variables.
• Polychrome has been replaced as a dependency by paletteer. Note that Polychrome::palette36 is still the default.

• run_app() now looks for columns that end with ‘_colors’ in their name which can be used to pre-specify colors for any companion variables. For example if you have spe$my_groups and spe$my_groups_colors then the second one can specify the colors that will be used for visualizing spe$my_groups. This makes specifying default colors more flexible than before, and the user is still free to change them if necessary.

                   Changes in version 1.7.17                        
  

BUG FIXES

• Fix bugs in layer_boxplot() where it was too specific to the Maynard et al 2021 data. We have made it more flexible now.

• Made the y-axis space more dynamic in gene_set_enrichment_plot() and layer_matrix_plot().

                   Changes in version 1.7.16                        
  

BUG FIXES

• Fixed a bug in sig_genes_extract() when there’s only one set of t-statistics or F statistics to extract.

                   Changes in version 1.7.12                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• The visualization functions vis_*() of SpatialLIBD in this version match the Bioconductor 3.15 version of SpatialExperiment. Note that if you used SpatialExperiment::read10xVisium(), the names of the spatial coordinates changed at https://github.com/drighelli/SpatialExperiment/commit/6710fe8b0a7919191ecce989bb6831647385ef5f and thus you might need to switch them back if you created your SpatialExperiment object before this change. You can do so with spatialCoordsNames(spe) <- rev(spatialCoordsNames(spe)). read10xVisiumWrapper() uses SpatialExperiment::read10xVisium() internally, so this change on SpatialExperiment would then also affect you.

                   Changes in version 1.7.11                        
  

NEW FEATURES

• Now layer_stat_cor() has the top_n argument which can be used for subsetting the marker genes prior to computing the correlation as part of the spatial registration process.

                   Changes in version 1.7.10                        
  

NEW FEATURES

• Added the add_key() function to reduce code duplication and resolve https://github.com/LieberInstitute/spatialLIBD/issues/31.

                    Changes in version 1.7.9                        
  

NEW FEATURES

• This version is now compatible with the bioc-devel version of SpatialExperiment where spatialData() was deprecated. Details at https://github.com/LieberInstitute/spatialLIBD/pull/29/files.

                    Changes in version 1.7.7                        
  

BUG FIXES

• Fixed a bug where the using the left-mouse click was not working for annotating individual spots under the “gene (interactive)” tab.

                    Changes in version 1.7.6                        
  

NEW FEATURES

• vis_gene_p(), vis_clus_p() and all related functions now have an argument point_size which lets you control how big the points are plotted. This can be useful for visualization purposes.
• The shiny app now has an input controlling the point size. If you increase it to say 5, then if you zoom in the clusters (interactive) panel, you can see larger spots when zooming in.

• These features are related to https://github.com/LieberInstitute/spatialLIBD/issues/28 although the spot diameter is still not the true spot diameter. However, now you have more flexibility for visualizing the spots.

                    Changes in version 1.7.5                        
  

NEW FEATURES

• Expanded the Using spatialLIBD with 10x Genomics public datasets vignette to show how you can deploy your web application. See https://libd.shinyapps.io/spatialLIBD_Human_Lymph_Node_10x/ for the live example.

                    Changes in version 1.7.4                        
  

BUG FIXES

• vis_gene() and vis_grid_gene() now support geneids that are found in the rownames(spe). This makese these functions more flexible.

• vis_grid_gene() and vis_grid_clus() now have the sample_order argument which gives you more control in case you want to plot a subset of samples. This should also reduced the memory required as discovered at https://github.com/LieberInstitute/spatialDLPFC/issues/45.

                    Changes in version 1.7.3                        
  

NEW FEATURES

• Added support for more than one background picture per sample. This was done through the new argument image_id. Resolves https://github.com/LieberInstitute/spatialLIBD/issues/25.
• Added options for side by side visualization of the background image and the clusters or gene expression values in the static versions. Resolves https://github.com/LieberInstitute/spatialLIBD/issues/19.
• Allow changing the transparency level of the spots with the alpha argument. Resolves https://github.com/LieberInstitute/spatialLIBD/issues/20.
• Add support for image manipulation with the magick package. Adds functions img_edit(), img_update() and img_update_all() as well as new features on the web application. Resolves https://github.com/LieberInstitute/spatialLIBD/issues/21.
• Added support for more control over the gene color scale and in the web application also added support for reversing the order of the scale. Resolves https://github.com/LieberInstitute/spatialLIBD/issues/22 and https://github.com/LieberInstitute/spatialLIBD/issues/23.
• Added export_cluster() and import_cluster() to help export/import clustering results instead of having to save large spe objects when exploring different clustering methods.

• Added locate_images() and add_images() for adding non-standard images to a spe object.

                    Changes in version 1.7.2                        
  

BUG FIXES

• Fixed an issue introduced by newer versions of shiny. This version of spatialLIBD works with shiny version 1.7.1, though it’s likely backwards compatible. Resolves https://github.com/LieberInstitute/spatialLIBD/issues/24.

• Fix an issue where as.data.frame(colData(spe)) uses check.names = TRUE by default and then changes the column names unintentionally.

                    Changes in version 1.7.1                        
  

NEW FEATURES

• Added read10xVisiumWrapper() and related functions that make it easier to read in the SpaceRanger output files and launch a shiny web application using run_app(). These new functions read in the analysis output from SpaceRanger by 10x Genomics, in particular, the clustering and dimension reduction (projection) results.

STexampleData

             Changes in version 1.3.3 (2022-01-31)                  

• add new datasets ST_mouseOB, SlideSeqV2_mouseHPC

• reformat datasets to SpatialExperiment version 1.5.2

tuberculosis

                    Changes in version 1.2.0                        

• GEO Series GSE126614 is now available through tuberculosis
• GEO Series GSE152532 is now available through tuberculosis
• GEO Series GSE174552 is now available through tuberculosis
• GEO Series GSE183912 is now available through tuberculosis
• GEO Series GSE184241 is now available through tuberculosis
• GEO Series GSE190024 is now available through tuberculosis
• GEO Series GSE190850 is now available through tuberculosis

NEWS from new and existing Workflows

GeoMxWorkflows

                    Changes in version 1.1.2                        

• Update install instructions, decrease R version, add links to other packages, ensure compatibility with updated GeomxTools

                    Changes in version 1.1.1                        
  

• Bug Fix: Header in vignette, remove self contained exception

Deprecated and Defunct Packages

Twenty one software packages were removed from this release (after being deprecated in Bioc 3.14): affyPara, ALPS, alsace, BrainStars, dualKS, ENCODExplorer, ENVISIONQuery, FindMyFriends, GeneAnswers, gramm4R, KEGGprofile, MSGFgui, MSGFplus, MSstatsTMTPTM, PanVizGenerator, predictionet, RGalaxy, scClassifR, slinky, SRGnet, SwimR

Please note: destiny and MouseFM, previously announced as deprecated in 3.14, fixed their packages and remained in Bioconductor.

Twenty nine software packages are deprecated in this release and will be removed in Bioc 3.16: ABAEnrichment, Autotuner, CAnD, caOmicsV, CHETAH, clonotypeR, CountClust, diffloop, GCSConnection, GCSFilesystem, GenoGAM, genphen, gprege, networkBMA, Onassis, perturbatr, phemd, ppiStats, ProteomicsAnnotationHubData, PSICQUIC, PubScore, Rgin, RmiR, RpsiXML, ScISI, SLGI, Sushi, tofsims, TSRchitect

Three experimental data packages were removed from this release (after being deprecated in BioC 3.14): ABAData, brainImageRdata, tcgaWGBSData.hg19

Please note: PCHiCdata and RITANdata previously announced as deprecated in 3.14, fixed their packages and remained in Bioconductor.

Three experimental data packages are deprecated in this release and will be removed in Bioc 3.16: DREAM4, MSstatsBioData, ppiData

One annotation packages was removed from this release (after being deprecated in Bioc 3.14): org.Pf.plasmo.db

Seven annotation packages were deprecated in this release and will be removed in Bioc 3.16: 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 workflow packages were removed from this release (after being deprecated in Bioc 3.14)

One workflow package was deprecated in this release and will be removed in 3.16: proteomics