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  • Bioconductor 3.21 Released

April 16, 2025

Bioconductor:

We are pleased to announce Bioconductor 3.21, consisting of 2341 software packages, 432 experiment data packages, 928 annotation packages, 30 workflows and 5 books.

There are 72 new software packages, 3 new data experiment packages, no new annotation packages, no new workflows, no new books, and many updates and improvements to existing packages.

Bioconductor 3.21 is compatible with R 4.5, and is supported on Linux, 64-bit Windows, Intel 64-bit macOS 11 (Big Sur) or higher, macOS arm64 and Linux arm64. This release will also include updated Bioconductor Docker containers.

Thank you to everyone for your contribution to Bioconductor

Visit Bioconductor BiocViews for details and downloads.

Contents

Getting Started with Bioconductor 3.21

To update to or install Bioconductor 3.21

  1. Install R 4.5. Bioconductor 3.21 has been designed expressly for this version of R.

  2. Follow the instructions at Installing Bioconductor.

New Software Packages

There are 72 new software packages in this release of Bioconductor.

  • alabaster.sfe Builds upon the existing ArtifactDB project, expending alabaster.spatial for language agnostic on disk serialization of SpatialFeatureExperiment.

  • barbieQ The barbieQ package provides a series of robust statistical tools for analysing barcode count data generated from cell clonal tracking (i.e., lineage tracing) experiments. In these experiments, an initial cell and its offspring collectively form a clone (i.e., lineage). A unique barcode sequence, incorporated into the DNA of the inital cell, is inherited within the clone. This one-to-one mapping of barcodes to clones enables clonal tracking of their behaviors. By counting barcodes, researchers can quantify the population abundance of individual clones under specific experimental perturbations. barbieQ supports barcode count data preprocessing, statistical testing, and visualization.

  • BatchSVG BatchSVG is a feature-based Quality Control (QC) to identify SVGs on spatial transcriptomics data with specific types of batch effect. Regarding to the spatial transcriptomics data experiments, the batch can be defined as “sample”, “sex”, and etc.The BatchSVG method is based on binomial deviance model (Townes et al, 2019) and applies cutoffs based on the number of standard deviation (nSD) of relative change in deviance and rank difference as the data-driven thresholding approach to detect the batch-biased outliers.

  • beachmat.tiledb Extends beachmat to initialize tatami matrices from TileDB-backed arrays. This allows C++ code in downstream packages to directly call the TileDB C/C++ library to access array data, without the need for block processing via DelayedArray. Developers only need to import this package to automatically extend the capabilities of beachmat::initializeCpp to TileDBArray instances.

  • bedbaser A client for BEDbase. bedbaser provides access to the API at api.bedbase.org. It also includes convenience functions to import BED files into GRanges objects and BEDsets into GRangesLists.

  • biocmake Manages the installation of CMake for building Bioconductor packages. This avoids the need for end-users to manually install CMake on their system. No action is performed if a suitable version of CMake is already available.

  • BreastSubtypeR BreastSubtypeR is an R package that provides a collection of methods for intrinsic molecular subtyping of breast cancer. It includes subtyping methods for nearest centroid-based subtyping (NC-based) and single sample predictor (SSP-based), along with tools for integrating clinical data and visualizing results.

  • BulkSignalR Inference of ligand-receptor (LR) interactions from bulk expression (transcriptomics/proteomics) data, or spatial transcriptomics. BulkSignalR bases its inferences on the LRdb database included in our other package, SingleCellSignalR available from Bioconductor. It relies on a statistical model that is specific to bulk data sets. Different visualization and data summary functions are proposed to help navigating prediction results.

  • CARDspa CARD is a reference-based deconvolution method that estimates cell type composition in spatial transcriptomics based on cell type specific expression information obtained from a reference scRNA-seq data. A key feature of CARD is its ability to accommodate spatial correlation in the cell type composition across tissue locations, enabling accurate and spatially informed cell type deconvolution as well as refined spatial map construction. CARD relies on an efficient optimization algorithm for constrained maximum likelihood estimation and is scalable to spatial transcriptomics with tens of thousands of spatial locations and tens of thousands of genes.

  • CCAFE Functions to reconstruct case and control AFs from summary statistics. One function uses OR, NCase, NControl, and SE(log(OR)). The second function uses OR, NCase, NControl, and AF for the whole sample.

  • chevreulPlot Tools for plotting SingleCellExperiment objects in the chevreulPlot package. Includes functions for analysis and visualization of single-cell data. Supported by NIH grants R01CA137124 and R01EY026661 to David Cobrinik.

  • chevreulProcess Tools analyzing SingleCellExperiment objects as projects. for input into the Chevreul app downstream. Includes functions for analysis of single cell RNA sequencing data. Supported by NIH grants R01CA137124 and R01EY026661 to David Cobrinik.

  • chevreulShiny Tools for managing SingleCellExperiment objects as projects. Includes functions for analysis and visualization of single-cell data. Also included is a shiny app for visualization of pre-processed scRNA data. Supported by NIH grants R01CA137124 and R01EY026661 to David Cobrinik.

  • clustSIGNAL clustSIGNAL: clustering of Spatially Informed Gene expression with Neighbourhood Adapted Learning. A tool for adaptively smoothing and clustering gene expression data. clustSIGNAL uses entropy to measure heterogeneity of cell neighbourhoods and performs a weighted, adaptive smoothing, where homogeneous neighbourhoods are smoothed more and heterogeneous neighbourhoods are smoothed less. This not only overcomes data sparsity but also incorporates spatial context into the gene expression data. The resulting smoothed gene expression data is used for clustering and could be used for other downstream analyses.

  • CPSM The CPSM package provides a comprehensive computational pipeline for predicting the survival probability of cancer patients. It offers a series of steps including data processing, splitting data into training and test subsets, and normalization of data. The package enables the selection of significant features based on univariate survival analysis and generates a LASSO prognostic index score. It supports the development of predictive models for survival probability using various features and provides visualization tools to draw survival curves based on predicted survival probabilities. Additionally, SPM includes functionalities for generating bar plots that depict the predicted mean and median survival times of patients, making it a versatile tool for survival analysis in cancer research.

  • crumblr Crumblr enables analysis of count ratio data using precision weighted linear (mixed) models. It uses an asymptotic normal approximation of the variance following the centered log ration transform (CLR) that is widely used in compositional data analysis. Crumblr provides a fast, flexible alternative to GLMs and GLMM’s while retaining high power and controlling the false positive rate.

  • crupR An R package that offers a workflow to predict condition-specific enhancers from ChIP-seq data. The prediction of regulatory units is done in four main steps: Step 1 - the normalization of the ChIP-seq counts. Step 2 - the prediction of active enhancers binwise on the whole genome. Step 3 - the condition-specific clustering of the putative active enhancers. Step 4 - the detection of possible target genes of the condition-specific clusters using RNA-seq counts.

  • dandelionR dandelionR is an R package for performing single-cell immune repertoire trajectory analysis, based on the original python implementation. It provides the necessary functions to interface with scRepertoire and a custom implementation of an absorbing Markov chain for pseudotime inference, inspired by the Palantir Python package.

  • DeconvoBuddies Funtions helpful for LIBD deconvolution project. Includes tools for marker finding with mean ratio, expression plotting, and plotting deconvolution results. Working to include DLPFC datasets.

  • DNAcycP2 This package performs prediction of intrinsic cyclizability of of every 50-bp subsequence in a DNA sequence. The input could be a file either in FASTA or text format. The output will be the C-score, the estimated intrinsic cyclizability score for each 50 bp sequences in each entry of the sequence set.

  • ELViS Base-resolution copy number analysis of viral genome. Utilizes base-resolution read depth data over viral genome to find copy number segments with two-dimensional segmentation approach. Provides publish-ready figures, including histograms of read depths, coverage line plots over viral genome annotated with copy number change events and viral genes, and heatmaps showing multiple types of data with integrative clustering of samples.

  • G4SNVHunter G-quadruplexes (G4s) are unique nucleic acid secondary structures predominantly found in guanine-rich regions and have been shown to be involved in various biological regulatory processes. G4SNVHunter is an R package designed to rapidly identify genomic sequences with G4-forming potential and accurately screen user-provided single nucleotide variants (also applicable to single nucleotide polymorphisms) that may destabilize these structures. This enables users to screen key variants for further experimental study, investigating how these variants may influence biological functions, such as gene regulation, by altering G4 formation.

  • geyser Lightweight Expression displaYer (plotter / viewer) of SummarizedExperiment object in R. This package provides a quick and easy Shiny-based GUI to empower a user to use a SummarizedExperiment object to view (gene) expression grouped from the sample metadata columns (in the colData slot). Feature expression can either be viewed with a box plot or a heatmap.

  • h5mread The main function in the h5mread package is h5mread(), which allows reading arbitrary data from an HDF5 dataset into R, similarly to what the h5read() function from the rhdf5 package does. In the case of h5mread(), the implementation has been optimized to make it as fast and memory-efficient as possible.

  • HiCParser This package is a parser to import HiC data into R. It accepts several type of data: tabular files, Cooler .cool or .mcool files, Juicer .hic files or HiC-Pro .matrix and .bed files. The HiC data can be several files, for several replicates and conditions. The data is formated in an InteractionSet object.

  • imageTCGA A Shiny application to explore the TCGA Diagnostic Image Database.

  • islify This software is meant to be used for classification of images of cell-based assays for neuronal surface autoantibody detection or similar techniques. It takes imaging files as input and creates a composite score from these, that for example can be used to classify samples as negative or positive for a certain antibody-specificity. The reason for its name is that I during its creation have thought about the individual picture as an archielago where we with different filters control the water level as well as ground characteristica, thereby finding islands of interest.

  • jazzPanda This package contains the function to find marker genes for image-based spatial transcriptomics data. There are functions to create spatial vectors from the cell and transcript coordiantes, which are passed as inputs to find marker genes. Marker genes are detected for every cluster by two approaches. The first approach is by permtuation testing, which is implmented in parallel for finding marker genes for one sample study. The other approach is to build a linear model for every gene. This approach can account for multiple samples and backgound noise.

  • Lheuristic The Lheuristic package identifies scatterpots that follow and L-shaped, negative distribution. It can be used to identify genes regulated by methylation by integration of an expression and a methylation array. The package uses two different methods to detect expression and methyaltion L- shapped scatterplots. The parameters can be changed to detect other scatterplot patterns.

  • limpa Quantification and differential analysis of mass-spectrometry proteomics data, with probabilistic recovery of information from missing values. Estimates the detection probability curve (DPC), which relates the probability of successful detection to the underlying expression level of each peptide, and uses it to incorporate peptide missing values into protein quantification and into subsequent differential expression analyses. The package produces objects suitable for downstream analysis in limma. The package accepts peptide-level data with missing values and produces complete protein quantifications without missing values. The uncertainty introduced by missing value imputation is propagated through to the limma analyses using variance modeling and precision weights. The package name “limpa” is an acronym for “Linear Models for Proteomics Data”.

  • LimROTS Differential expression analysis is a prevalent method utilised in the examination of diverse biological data. The reproducibility-optimized test statistic (ROTS) modifies a t-statistic based on the data’s intrinsic characteristics and ranks features according to their statistical significance for differential expression between two or more groups (f-statistic). Focussing on proteomics and metabolomics, the current ROTS implementation cannot account for technical or biological covariates such as MS batches or gender differences among the samples. Consequently, we developed LimROTS, which employs a reproducibility-optimized test statistic utilising the limma methodology to simulate complex experimental designs. LimROTS is a hybrid method integrating empirical bayes and reproducibility-optimized statistics for robust analysis of proteomics and metabolomics data.

  • maaslin3 MaAsLin 3 refines and extends generalized multivariate linear models for meta-omicron association discovery. It finds abundance and prevalence associations between microbiome meta-omics features and complex metadata in population-scale epidemiological studies. The software includes multiple analysis methods (including support for multiple covariates, repeated measures, and ordered predictors), filtering, normalization, and transform options to customize analysis for your specific study.

  • MetaboDynamics MetaboDynamics is an R-package that provides a framework of probabilistic models to analyze longitudinal metabolomics data. It enables robust estimation of mean concentrations despite varying spread between timepoints and reports differences between timepoints as well as metabolite specific dynamics profiles that can be used for identifying “dynamics clusters” of metabolites of similar dynamics. Provides probabilistic over-representation analysis of KEGG functional modules and pathways as well as comparison between clusters of different experimental conditions.

  • miaDash miaDash provides a Graphical User Interface for the exploration of microbiome data. This way, no knowledge of programming is required to perform analyses. Datasets can be imported, manipulated, analysed and visualised with a user-friendly interface.

  • mist mist (Methylation Inference for Single-cell along Trajectory) is a hierarchical Bayesian framework for modeling DNA methylation trajectories and performing differential methylation (DM) analysis in single-cell DNA methylation (scDNAm) data. It estimates developmental-stage-specific variations, identifies genomic features with drastic changes along pseudotime, and, for two phenotypic groups, detects features with distinct temporal methylation patterns. mist uses Gibbs sampling to estimate parameters for temporal changes and stage-specific variations.

  • mitology mitology allows to study the mitochondrial activity throught high-throughput RNA-seq data. It is based on a collection of genes whose proteins localize in to the mitochondria. From these, mitology provides a reorganization of the pathways related to mitochondria activity from Reactome and Gene Ontology. Further a ready-to-use implementation of MitoCarta3.0 pathways is included.

  • MotifPeeker MotifPeeker is used to compare and analyse datasets from epigenomic profiling methods with motif enrichment as the key benchmark. The package outputs an HTML report consisting of three sections: (1. General Metrics) Overview of peaks-related general metrics for the datasets (FRiP scores, peak widths and motif-summit distances). (2. Known Motif Enrichment Analysis) Statistics for the frequency of user-provided motifs enriched in the datasets. (3. De-Novo Motif Enrichment Analysis) Statistics for the frequency of de-novo discovered motifs enriched in the datasets and compared with known motifs.

  • mspms This package provides functions for the analysis of data generated by the multiplex substrate profiling by mass spectrometry for proteases (MSP-MS) method. Data exported from upstream proteomics software is accepted as input and subsequently processed for analysis. Tools for statistical analysis, visualization, and interpretation of the data are provided.

  • MSstatsBioNet A set of tools for network analysis using mass spectrometry-based proteomics data and network databases. The package takes as input the output of MSstats differential abundance analysis and provides functions to perform enrichment analysis and visualization in the context of prior knowledge from past literature. Notably, this package integrates with INDRA, which is a database of biological networks extracted from the literature using text mining techniques.

  • OSTA.data ‘OSTA.data’ is a companion package for the “Orchestrating Spatial Transcriptomics Analysis” (OSTA) with Bioconductor online book. Throughout OSTA, we rely on a set of publicly available datasets that cover different sequencing- and imaging-based platforms, such as Visium, Visium HD, Xenium (10x Genomics) and CosMx (NanoString). In addition, we rely on scRNA-seq (Chromium) data for tasks, e.g., spot deconvolution and label transfer (i.e., supervised clustering). These data been deposited in an Open Storage Framework (OSF) repository, and can be queried and downloaded using functions from the ‘osfr’ package. For convenience, we have implemented ‘OSTA.data’ to query and retrieve data from our OSF node, and cache retrieved Zip archives using ‘BiocFileCache’.

  • pathMED PathMED is a collection of tools to facilitate precision medicine studies with omics data (e.g. transcriptomics). Among its funcionalities, genesets scores for individual samples may be calculated with several methods. These scores may be used to train machine learning models and to predict clinical features on new data. For this, several machine learning methods are evaluated in order to select the best method based on internal validation and to tune the hyperparameters. Performance metrics and a ready-to-use model to predict the outcomes for new patients are returned.

  • PICB piRNAs (short for PIWI-interacting RNAs) and their PIWI protein partners play a key role in fertility and maintaining genome integrity by restricting mobile genetic elements (transposons) in germ cells. piRNAs originate from genomic regions known as piRNA clusters. The piRNA Cluster Builder (PICB) is a versatile toolkit designed to identify genomic regions with a high density of piRNAs. It constructs piRNA clusters through a stepwise integration of unique and multimapping piRNAs and offers wide-ranging parameter settings, supported by an optimization function that allows users to test different parameter combinations to tailor the analysis to their specific piRNA system. The output includes extensive metadata columns, enabling researchers to rank clusters and extract cluster characteristics.

  • poem This package provides a comprehensive set of external and internal evaluation metrics. It includes metrics for assessing partitions or fuzzy partitions derived from clustering results, as well as for evaluating subpopulation identification results within embeddings or graph representations. Additionally, it provides metrics for comparing spatial domain detection results against ground truth labels, and tools for visualizing spatial errors.

  • Polytect Polytect is an advanced computational tool designed for the analysis of multi-color digital PCR data. It provides automatic clustering and labeling of partitions into distinct groups based on clusters first identified by the flowPeaks algorithm. Polytect is particularly useful for researchers in molecular biology and bioinformatics, enabling them to gain deeper insights into their experimental results through precise partition classification and data visualization.

  • QRscore In genomics, differential analysis enables the discovery of groups of genes implicating important biological processes such as cell differentiation and aging. Non-parametric tests of differential gene expression usually detect shifts in centrality (such as mean or median), and therefore suffer from diminished power against alternative hypotheses characterized by shifts in spread (such as variance). This package provides a flexible family of non-parametric two-sample tests and K-sample tests, which is based on theoretical work around non-parametric tests, spacing statistics and local asymptotic normality (Erdmann-Pham et al., 2022+ [arXiv:2008.06664v2]; Erdmann-Pham, 2023+ [arXiv:2209.14235v2]).

  • RbowtieCuda This package provides an R wrapper for the popular Bowtie2 sequencing read aligner, optimized to run on NVIDIA graphics cards. It includes wrapper functions that enable both genome indexing and alignment to the generated indexes, ensuring high performance and ease of use within the R environment.

  • ReducedExperiment Provides SummarizedExperiment-like containers for storing and manipulating dimensionally-reduced assay data. The ReducedExperiment classes allow users to simultaneously manipulate their original dataset and their decomposed data, in addition to other method-specific outputs like feature loadings. Implements utilities and specialised classes for the application of stabilised independent component analysis (sICA) and weighted gene correlation network analysis (WGCNA).

  • RFLOMICS R-package with shiny interface, provides a framework for the analysis of transcriptomics, proteomics and/or metabolomics data. The interface offers a guided experience for the user, from the definition of the experimental design to the integration of several omics table together. A report can be generated with all settings and analysis results.

  • Rigraphlib Vendors the igraph C source code and builds it into a static library. Other Bioconductor packages can link to libigraph.a in their own C/C++ code. This is intended for packages wrapping C/C++ libraries that depend on the igraph C library and cannot be easily adapted to use the igraph R package.

  • rigvf The IGVF Catalog provides data on the impact of genomic variants on function. The rigvf package provides an interface to the IGVF Catalog, allowing easy integration with Bioconductor resources.

  • RUCova Mass cytometry enables the simultaneous measurement of dozens of protein markers at the single-cell level, producing high dimensional datasets that provide deep insights into cellular heterogeneity and function. However, these datasets often contain unwanted covariance introduced by technical variations, such as differences in cell size, staining efficiency, and instrument-specific artifacts, which can obscure biological signals and complicate downstream analysis. This package addresses this challenge by implementing a robust framework of linear models designed to identify and remove these sources of unwanted covariance. By systematically modeling and correcting for technical noise, the package enhances the quality and interpretability of mass cytometry data, enabling researchers to focus on biologically relevant signals.

  • scHiCcompare This package provides functions for differential chromatin interaction analysis between two single-cell Hi-C data groups. It includes tools for imputation, normalization, and differential analysis of chromatin interactions. The package implements pooling techniques for imputation and offers methods to normalize and test for differential interactions across single-cell Hi-C datasets.

  • scQTLtools This package specializes in analyzing and visualizing eQTL at the single-cell level. It can read gene expression matrices or Seurat data, or SingleCellExperiment object along with genotype data. It offers a function for cis-eQTL analysis to detect eQTL within a given range, and another function to fit models with three methods. Using this package, users can also generate single-cell level visualization result.

  • SEraster SEraster is a rasterization preprocessing framework that aggregates cellular information into spatial pixels to reduce resource requirements for spatial omics data analysis. SEraster reduces the number of spatial points in spatial omics datasets for downstream analysis through a process of rasterization where single cells’ gene expression or cell-type labels are aggregated into equally sized pixels based on a user-defined resolution. SEraster is built on an R/Bioconductor S4 class called SpatialExperiment. SEraster can be incorporated with other packages to conduct downstream analyses for spatial omics datasets, such as detecting spatially variable genes.

  • shinyDSP This package is a Shiny app for interactively analyzing and visualizing Nanostring GeoMX Whole Transcriptome Atlas data. Users have the option of exploring a sample data to explore this app’s functionality. Regions of interest (ROIs) can be filtered based on any user-provided metadata. Upon taking two or more groups of interest, all pairwise and ANOVA-like testing are automatically performed. Available ouputs include PCA, Volcano plots, tables and heatmaps. Aesthetics of each output are highly customizable.

  • Site2Target Statistics implemented for both peak-wise and gene-wise associations. In peak-wise associations, the p-value of the target genes of a given set of peaks are calculated. Negative binomial or Poisson distributions can be used for modeling the unweighted peaks targets and log-nromal can be used to model the weighted peaks. In gene-wise associations a table consisting of a set of genes, mapped to specific peaks, is generated using the given rules.

  • smoppix Test for univariate and bivariate spatial patterns in spatial omics data with single-molecule resolution. The tests implemented allow for analysis of nested designs and are automatically calibrated to different biological specimens. Tests for aggregation, colocalization, gradients and vicinity to cell edge or centroid are provided.

  • sosta sosta (Spatial Omics STructure Analysis) is a package for analyzing spatial omics data to explore tissue organization at the anatomical structure level. It reconstructs anatomically relevant structures based on molecular features or cell types. It further calculates a range of metrics at the structure level to quantitatively describe tissue architecture. The package is designed to integrate with other packages for the analysis of spatial omics data.

  • spacexr Spatial-eXpression-R (spacexr) is a package for analyzing cell types in spatial transcriptomics data. This implementation is a fork of the spacexr GitHub repo (https://github.com/dmcable/spacexr), adapted to work with Bioconductor objects. The original package implements two statistical methods: RCTD for learning cell types and CSIDE for inferring cell type-specific differential expression. Currently, this fork only implements RCTD, which learns cell type profiles from annotated RNA sequencing (RNA-seq) reference data and uses these profiles to identify cell types in spatial transcriptomic pixels while accounting for platform-specific effects. Future releases will include an implementation of CSIDE.

  • SpatialExperimentIO Read in imaging-based spatial transcriptomics technology data. Current available modules are for Xenium by 10X Genomics, CosMx by Nanostring, MERSCOPE by Vizgen, or STARmapPLUS from Broad Institute. You can choose to read the data in as a SpatialExperiment or a SingleCellExperiment object.

  • spatialFDA spatialFDA is a package to calculate spatial statistics metrics. The package takes a SpatialExperiment object and calculates spatial statistics metrics using the package spatstat. Then it compares the resulting functions across samples/conditions using functional additive models as implemented in the package refund. Furthermore, it provides exploratory visualisations using functional principal component analysis, as well implemented in refund.

  • SplineDV A spline based scRNA-seq method for identifying differentially variable (DV) genes across two experimental conditions. Spline-DV constructs a 3D spline from 3 key gene statistics: mean expression, coefficient of variance, and dropout rate. This is done for both conditions. The 3D spline provides the “expected” behavior of genes in each condition. The distance of the observed mean, CV and dropout rate of each gene from the expected 3D spline is used to measure variability. As the final step, the spline-DV method compares the variabilities of each condition to identify differentially variable (DV) genes.

  • SVP SVP uses the distance between cells and cells, features and features, cells and features in the space of MCA to build nearest neighbor graph, then uses random walk with restart algorithm to calculate the activity score of gene sets (such as cell marker genes, kegg pathway, go ontology, gene modules, transcription factor or miRNA target sets, reactome pathway, …), which is then further weighted using the hypergeometric test results from the original expression matrix. To detect the spatially or single cell variable gene sets or (other features) and the spatial colocalization between the features accurately, SVP provides some global and local spatial autocorrelation method to identify the spatial variable features. SVP is developed based on SingleCellExperiment class, which can be interoperable with the existing computing ecosystem.

  • TaxSEA TaxSEA is an R package for Taxon Set Enrichment Analysis, which utilises a Kolmogorov-Smirnov test analyses to investigate differential abundance analysis output for whether there are alternations in a-priori defined sets of taxa from five previously published databases (BugSigDB, MiMeDB, GutMGene, mBodyMap and GMRepoV2). TaxSEA takes as input a list of taxonomic identifiers (e.g. species names, NCBI IDs etc.) and a rank (E.g. fold change, correlation coefficient). TaxSEA be applied to any microbiota taxonomic profiling technology (array-based, 16S rRNA gene sequencing, shotgun metagenomics & metatranscriptomics etc.) and enables researchers to rapidly contextualize their findings within the broader literature to accelerate interpretation of results.

  • TENET TENET identifies key transcription factors (TFs) and regulatory elements (REs) linked to a specific cell type by finding significantly correlated differences in gene expression and RE methylation between case and control input datasets, and identifying the top genes by number of significant RE DNA methylation site links. It also includes many additional tools to aid in visualization and analysis of the results, including plots displaying and comparing methylation and expression data and RE DNA methylation site link counts, survival analysis, TF motif searching in the vicinity of linked RE DNA methylation sites, custom TAD and peak overlap analysis, and UCSC Genome Browser track file generation. A utility function is also provided to download methylation, expression, and patient survival data from The Cancer Genome Atlas (TCGA) for use in TENET or other analyses.

  • terapadog This package performs a Gene Set Analysis with the approach adopted by PADOG on the genes that are reported as translationally regulated (ie. exhibit a significant change in TE) by the DeltaTE package. It can be used on its own to see the impact of translation regulation on gene sets, but it is also integrated as an additional analysis method within ReactomeGSA, where results are further contextualised in terms of pathways and directionality of the change.

  • TrIdent The TrIdent R package automates the analysis of transductomics data by detecting, classifying, and characterizing read coverage patterns associated with potential transduction events. Transductomics is a DNA sequencing-based method for the detection and characterization of transduction events in pure cultures and complex communities. Transductomics relies on mapping sequencing reads from a viral-like particle (VLP)-fraction of a sample to contigs assembled from the metagenome (whole-community) of the same sample. Reads from bacterial DNA carried by VLPs will map back to the bacterial contigs of origin creating read coverage patterns indicative of ongoing transduction.

  • visiumStitched This package provides helper functions for working with multiple Visium capture areas that overlap each other. This package was developed along with the companion example use case data available from https://github.com/LieberInstitute/visiumStitched_brain. visiumStitched prepares SpaceRanger (10x Genomics) output files so you can stitch the images from groups of capture areas together with Fiji. Then visiumStitched builds a SpatialExperiment object with the stitched data and makes an artificial hexogonal grid enabling the seamless use of spatial clustering methods that rely on such grid to identify neighboring spots, such as PRECAST and BayesSpace. The SpatialExperiment objects created by visiumStitched are compatible with spatialLIBD, which can be used to build interactive websites for stitched SpatialExperiment objects. visiumStitched also enables casting SpatialExperiment objects as Seurat objects.

  • vmrseq High-throughput single-cell measurements of DNA methylation allows studying inter-cellular epigenetic heterogeneity, but this task faces the challenges of sparsity and noise. We present vmrseq, a statistical method that overcomes these challenges and identifies variably methylated regions accurately and robustly.

  • XAItest XAItest is an R Package that identifies features using eXplainable AI (XAI) methods such as SHAP or LIME. This package allows users to compare these methods with traditional statistical tests like t-tests, empirical Bayes, and Fisher’s test. Additionally, it includes a system that enables the comparison of feature importance with p-values by incorporating calibrated simulated data.

  • xCell2 xCell2 provides methods for cell type enrichment analysis using cell type signatures. It includes three main functions - 1. xCell2Train for training custom references objects from bulk or single-cell RNA-seq datasets. 2. xCell2Analysis for conducting the cell type enrichment analysis using the custom reference. 3. xCell2GetLineage for identifying dependencies between different cell types using ontology.

  • XeniumIO The package allows users to readily import spatial data obtained from the 10X Xenium Analyzer pipeline. Supported formats include ‘parquet’, ‘h5’, and ‘mtx’ files. The package mainly represents data as SpatialExperiment objects.

New Data Experiment Packages

There are 3 new data experiment packages in this release of Bioconductor.

  • humanHippocampus2024 This is an ExperimentHub Data package that helps to access the spatially-resolved transcriptomics and single-nucleus RNA sequencing data. The datasets are generated from adjacent tissue sections of the anterior human hippocampus across ten adult neurotypical donors. The datasets are based on spatial_hpc project by Lieber Institute for Brain Development (LIBD) researchers and collaborators.

  • muSpaData Data package containing a multi-sample multi-group spatial dataset in SpatialExperiment Bioconductor object format.

  • TENET.ExperimentHub ExperimentHub package containing datasets for use in the TENET package’s vignette and function examples. These include a variety of different objects to illustrate different datasets used in TENET functions. Where applicable, all datasets are aligned to the hg38 human genome.

New Annotation Packages

There are no new annotation packages in this release of Bioconductor.

New Workflow Packages

There are no new workflow packages in this release of Bioconductor.

New Online Books

There are no new books in this release of Bioconductor.

NEWS from existing Software Packages

ADaCGH2

             Changes in version 2.47.2 (2025-04-08)

  • Updated NEWS: Removed dependency on GLAD: GLAD was failing in 2025-02 on all platforms on BioC 3.21; it is now an Enhances.

               Changes in version 2.47.1 (2025-02-19)

  • Removed dependency on GLAD. GLAD fails in all platforms on BioC 3.21.

affxparser

             Changes in version 1.79.1 (2025-01-06)

Bug Fixes

  • The package failed to compile in R-devel (to become R 4.5.0). This i because the C-level API of R is being tidied up and now requiring the R_ and Rf_ prefixes to be used. For example, R_Calloc() should be used instead of Calloc(), and Rf_allocVector() should be used instead of allocVector().

               Changes in version 1.79.0 (2024-10-30)

Notes

  • The version number was bumped for the Bioconductor develop version, which is now Bioconductor 3.21 for R (>= 4.5).

alabaster.base

                    Changes in version 1.8.0

  • Added createDedupSession(), addObjectToDedupSession() and checkObjectInDedupSession() utilities, that allow saveObject() method developers to check for duplicated objects and avoid re-saving them. Most of this functionality was migrated and generalized from the alabaster.matrix package.

  • Added the cloneDirectory() function to easily clone the contents of an existing directory, either by copying or linking to the files. This should be used for creating lightweight on-disk representations of duplicated objects.

  • Added the absolutizePath() function to obtain an absolute file path. This is occasionally necessary to ensure that references to deduplicated resources are robust to changes to the working directory.

  • Coerce numeric_version instances to strings or character vectors before saving them in saveObject(). This includ such objects encountered inside lists or DataFrames.

  • Added getSaveEnvironment() and related functions to keep track of the R environment used to save each object. This facilitates debugging and enables corrective actions to be taken by loading functions when encountering files created by buggy versions of any package in the alabaster stack.

  • Added preliminary support for custom variable length string (VLS) arrays, which compress the heap for more efficient storage than HDF5’s VLS implementation. This is enabled in the saveObject() methods for standalone character vectors as well as character vectors in DataFrames and lists via the relevant character.vls= option. Setting character.vls=NULL will automatically switch between fixed-length string datasets and VLS arrays based on the estimated storage. (Defaults to FALSE for back-compatibility.)

alabaster.matrix

                    Changes in version 1.8.0

  • Deprecated the WrapperArraySeed in favor of direct inheritance from DelayedUnaryIsoOp.

  • Support deduplication of arrays and sparse matrices via the new array.dedup.session= argument in their corresponding saveObject() methods. This also allows deduplication of external DelayedArray seeds if they have already been processed outside a DelayedArray in the same session.

  • Added a DelayedArray.force.external= argument to the saveObject() method for DelayedArrays. This is a more convenient way of forcing seeds to be saved as external arrays for deduplication.

  • Support the new custom variable length string format for storing character arrays in HDF5. This is controlled by the array.character.vls= option in the array’s saveObject() method.

AnVIL

                   Changes in version 1.20.0

USER VISIBLE CHANGES

  • (v 1.19.5) Added host slot to Service class slot to show any subdomains in the API host URL.

  • (v 1.19.1) Deprecated av*, gcloud, etc. functions are now defunct; see *-defunct documentation pages.

BUG FIXES AND MINOR IMPROVEMENTS

  • (v 1.19.9) Trigger updates based on changes to Dockstore API

  • (v 1.19.7) Updated NEWS.md and GitHub Actions to automate version updates in Dockstore.

  • (v 1.19.6) Remove test meant for rapiclient client package.

  • (v 1.19.4) Update Dockstore API version

  • (v 1.19.3) Remove examples and tests for defunct functions.

  • (v 1.19.2) Use gcloud_exists from the AnVILGCP package.

AnVILGCP

                    Changes in version 1.2.0

New features

  • Remove defunct drs_stat, drs_access_url, and drs_cp functions
  • Defunct bucket_location and bucket arguments

Bug fixes and minor improvements

  • Filter out “prerequisites” element from response (#103)
  • Clean up unused authenticate_* code
  • Remove httr2 from Suggests

ATACseqQC

                   Changes in version 1.31.1
  • Update email address.

ATACseqTFEA

                    Changes in version 1.9.1
  • update email address.

bandle

                    Changes in version 1.11

Changes in version bandle 1.11.1

  • Use C++14

Changes in version bandle 1.11.0

  • push to Bioc devel

basilisk.utils

                   Changes in version 1.20.0

  • Detect the BASILISK_EXTERNAL_FALLBACK_R environment to use an external fallback R environment.

  • Updated to the latest version of the Miniforge installer (24.11.3-0).

  • Updated the version of reticulate in the fallback R environment to 1.40.0.

  • Expose the default version of the Miniforge installation via the new defaultMiniforgeVersion constant.

BatchQC

                    Changes in version 2.2.5

Minor Changes

  • Added sva batch correction method (for unknown variation correction)

                      Changes in version 2.2.4

Major Changes

  • Updated variation ratio analysis to be log transformed

  • Added umap exploratory option

                      Changes in version 2.2.3

Major Changes

  • Added limma as a batch correction
  • Added umap plot option
  • Added ellipses to pca plot

Minor Changes

  • Set p-val plot x scale to always be 0 to 1

  • Removed Intercept from p-val violin plots

                      Changes in version 2.2.2

Minor Changes

  • Updated SE object upload to allow assays of any name (no longer require one assay to be called “counts”)

                      Changes in version 2.2.1

Minor Changes

  • Added pval information to the DESeq2 binomial evaluation

beachmat

                   Changes in version 2.24.0

  • Automatically cast integer/logical NAs to their double equivalents in the matrices wrapped by initializeCpp(). This can be disabled by setting .check.na=FALSE.

  • Added a initializeCpp() method for the ConstantArraySeed class.

  • Using a TileDBArraySeed in initializeCpp() now automatically dispatches to beachmat.tiledb.

benchdamic

             Changes in version 1.13.1 (2024-11-20)

  • Bug-fix: changed an internal parameter of DA_ANCOM() to make it works after the new release

               Changes in version 1.13.0 (2024-10-29)

  • Bump x.y.z version to odd y following creation of RELEASE_3_20 branch

               Changes in version 1.12.1 (2024-11-20)

  • Porting the changes of devel version 1.13.1 to release

BiocCheck

                   Changes in version 1.44.0

NEW FEATURES

  • Add lifeCycle, deprecate_warn, and deprecate_stop to the list of functions for the .Deprecated / .Defunct check.

  • Support checking \() syntax as anonymous R functions.

  • Exclude comment-only lines in function lengths check (@hpages, #220)

  • Add checkFndPerson() to validate Authors@R / Authors fields in the DESCRIPTION file. A corresponding NOTE is shown in the vignette (#215)

  • Refactor function length check to count only coding lines and not comment lines (@hpages, #220)

BUG FIXES AND MINOR IMPROVEMENTS

  • Check file sizes only for source directories and in BiocCheckGitClone (@hpages, #219)

  • Use R version from BiocManager:::.version_map for checkRVersionDependency (@helenalc, #223)

  • Use checkInstalled() to verify packages listed in Suggests:

  • Suppress warning in .hasPkg() when the package is not installed

  • Use INFO messages instead of bullet points in output

BiocFileCache

                    Changes in version 2.15

BUG FIX

  • (2.15.1) Fix issue trying to create multiple caches in single R session

BiocGenerics

                   Changes in version 0.54.0

NEW FEATURES

  • Add longForm() S4 generic. See https://github.com/waldronlab/MultiAssayExperiment/issues/333 for some context.

  • Add paste2() S4 generic, with methods defined for ordinary vectors and arrays. Also add add_prefix() and add_suffix(), two simple wrappers around paste2() provided for convenience and code readability.

  • Define setequal() S4 generic with generics::setequal as default method.

SIGNIFICANT USER-VISIBLE CHANGES

  • Add CRAN package generics to Depends field. The default methods for S4 generics union(), intersect(), and setdiff() now are generics::union(), generics::intersect(), and generics::setdiff(), respectively. See ‘?BiocGenerics::setops’ for more information.

BiocHubsShiny

                    Changes in version 1.8.0

Significant user-visible changes

  • Save the table of result to a text file instead of Rds.
  • Use a helper function to link images to the vignette from either online or local sources
  • Add a README.md file

Bug fixes and minor improvements

  • Added a clipboard icon to the shinyAce editor to allow copying the code to the clipboard.
  • Include package anchors in documentation links
  • Import write.table from the utils package

BiocParallel

                    Changes in version 1.42

BUG FIXES

BiocPkgTools

                   Changes in version 1.26.0

SIGNIFICANT USER-VISIBLE CHANGES

  • Defunct pkgType = "all" argument in biocDownloadStats and biocRevDepEmail

  • Added R (>= 4.1.0) requirement and replaced usage of %>% (magrittr) with native pipe |> throughout the package

  • Removed dependency on the magrittr package

BUG FIXES AND MINOR IMPROVEMENTS

  • Filter URLs with helper function that checks availability in biocBuildReportDB

  • Always use .CRAN_WEB_URL in CRAN_pkg_rds_url() helper

  • Updated getPkgYearsInBioc() and documentation

  • Reformatted output from anacondaDownloadStats()

biocthis

                   Changes in version 1.17.4

NEW FEATURES

  • use_bioc_github_action() now creates a .github/workflows/bioc-check.yml file that has the option ‘bioc_version’ set to “bioc-release” by default. It can also take the values “bioc-devel” or a specific Bioconductor version number in the X.YY format such as “3.20”. This updated GitHub Actions workflow aims to be as static as possible across Bioconductor release versions. Meaning that in the future you won’t need to use use_bioc_github_action() again to update the GHA workflow after every Bioconductor release. This was motivated by the “dynamic matrix generation” documentation available at https://runs-on.com/github-actions/the-matrix-strategy/#dynamic-matrix-generation. For a detailed explanation of the changes in this version, check the LIBD RStats club presentation “[2025-03-21] biocthis v1.17.4 updated GitHub Actions workflow”. The video is available at https://www.youtube.com/watch?v=bzzPBt3Mz0A and the notes at https://docs.google.com/document/d/1z8xkC_3kAsGlpF_UyM9YfV-08o1lTer7xoBz2lQ1IjY/edit?usp=sharing.

                     Changes in version 1.17.3

SIGNIFICANT USER-VISIBLE CHANGES

  • use_bioc_github_action() now uses simpler code for caching R packages across GitHub Action runs. This code won’t need to be updated across versions, meaning that it’ll be easier to update the .github/workflows/check-bioc.yml file across Bioconductor versions. Also, @gaborcsardi’s recent commit to r-lib/actions as noted at https://github.com/r-lib/actions/issues/912#issuecomment-2667950006 gave me a hint on how to simplify code across macOS/winOS and linux for the caching of R packages. Also, note that thanks to https://github.com/r-lib/remotes/commit/0e4e23051041d9f1b15a5ab796defec31af6190d we will soon be able to re-enable automatic installation of linux system dependencies thanks to remotes::system_requirements(“ubuntu”, “24.04”) being supported in the near future. Finally, we no longer need to specify RSPM although there are detailed instructions at https://packagemanager.posit.co/client/#/repos/bioconductor/setup on how to do so.

                     Changes in version 1.17.2

SIGNIFICANT USER-VISIBLE CHANGES

  • use_bioc_description() now has report_bioc set to FALSE by default to match the Bioconductor guidelines listed at https://contributions.bioconductor.org/description.html#description-bugreport. This was brought up in a December 2024 package review at https://github.com/Bioconductor/Contributions/issues/3503#issuecomment-2551233199.
  • Similarly, use_bioc_pkg_templates() now adds the dev/ directory to the main .gitignore file. This was also brought up in the same package review.
  • use_bioc_vignette() no longer creates a vignettes/.gitignore file. The rendered .R and .html files are instead ignored on the package main .gitignore file. This complies with the request from that same package review while also keeping in line with the behavior from usethis::use_vignette() https://github.com/r-lib/usethis/blob/a653d6e05f9172772cea1055f8415cda2f26de69/R/vignette.R#L11-L12.

  • use_bioc_vignette()’s template no longer tracks how much time was used to render the vignette, nor shows the code used for obtaining the .R file with knit(tangle = TRUE), nor the date the vignette was generated. This was also brought up in the same package review from December 2024, as well as in a second one from October 2024 at https://github.com/Bioconductor/Contributions/issues/3501#issuecomment-2408081535.

                     Changes in version 1.17.1

SIGNIFICANT USER-VISIBLE CHANGES

  • use_bioc_github_action() now uses the actions/cache@v4 instead of v3.

biomaRt

                   Changes in version 2.64.0

BUG FIXES

  • Version 1.10 of {httr2} changed how URLs are parsed, and this broke some biomaRt functionality. This has been patched. (Backported to biomaRt 2.62.1)

BioNAR

                    Changes in version 1.9.2
  • Basic clustering is component wise now. That means that before clustering algorithm application graph split into weak components, to which clustering algorithms applied independently. If algorithm fails on some component, whole component considered as a cluster.

Biostrings

                   Changes in version 2.76.0

NEW FEATURES

  • Add functions update_DNA_palette(), update_RNA_palette(), update_AA_palette(), and update_B_palette(), to let users set their own color palettes for XString/XStringSet objects. Author: Aidan Lakshman

SIGNIFICANT USER-VISIBLE CHANGES

  • Bring back the BLOSUM* and PAM* scoring matrices from pwalign but now they display a warning that their new home is the pwalign package and that they will soon be removed from the Biostrings package.

DEPRECATED AND DEFUNCT

  • Deprecate XStringPartialMatches objects. They’ve been a stale work-in-progress since 2008 so time to get rid of them!

  • Formally deprecate all the functions that went to pwalign in BioC 3.19.

BreastSubtypeR

                    Changes in version 1.0.0

Major changes

  • Initial release of the BreastSubtypeR package.
  • Implements NC-based and SSP-based molecular subtyping methods for breast cancer.
  • Provides an R Shiny app for users unfamiliar with R.

Features

  • Comprehensive Intrinsic Subtyping for Breast Cancer: Integrates multiple published intrinsic subtyping methods, including NC-based approaches like the original PAM50 (Parker et al., J Clin Oncol, 2009) and SSP-based methods like AIMS (Paquet et al., J Natl Cancer Inst, 2015).
  • Multi-Method Subtyping Functionality: Simultaneously predicts breast cancer intrinsic subtypes using a variety of validated methods for comparative analysis.
  • AUTO Mode Feature: Evaluates the distribution of ER and HER2 status in the test cohort to automatically select subtyping methods that align with the cohort’s characteristics, ensuring compatibility with method-specific assumptions for greater accuracy and reliability.
  • Optimized Gene Mapping: Optimizes gene mapping using Entrez IDs to maximize the inclusion of genes across subtyping methods.
  • Streamlined Input and Output: Provides standardized input/output formats to ensure smooth integration with other gene expression analysis tools.
  • User-Friendly Shiny App Interface: Features a web-based GUI that runs entirely locally, ensuring data privacy with no online sharing, ideal for users who prefer a visual interface over R scripting.

BridgeDbR

                   Changes in version 2.17.1
  • Updated to BridgeDb 3.0.28
  • Added CiTO annotation to the vignette (not visible in the HTML)
  • Added session info to the vignette

BSgenome

                   Changes in version 1.76.0

DEPRECATED AND DEFUNCT

  • Formally deprecate BSgenome::forgeMasksFile, BSgenome::forgeSeqFiles, BSgenome::forgeSeqlengthsRdaFile, BSgenome::forgeSeqlengthsRdsFile, BSgenome::forgeBSgenomeDataPkg, and BSgenome::forgeMaskedBSgenomeDataPkg. All these functions are now defined in the BSgenomeForge package.

BSgenomeForge

                    Changes in version 1.8.0
  • No significant changes in this version.

bugsigdbr

                   Changes in version 1.13.6

  • Add domain support for signatures

                     Changes in version 1.13.2

  • Update functions to accommodate PMID as Study ID

Cardinal

             Changes in version 3.8.3 (2024-12-18)

BUG FIXES

  • Fix error in ‘selectROI()’ for whole-experiment images

               Changes in version 3.8.2 (2024-12-11)

SIGNIFICANT USER-VISIBLE CHANGES

  • Update ‘peakAlign()’ with ‘binfun’ parameter

  • Previous (3.6) behavior corresponds to ‘binfun=”median”’

BUG FIXES

  • Fix error in ‘peakAlign()’ for high resolution peaks

  • Set minimum relative alignment resolution of 0.5 ppm

  • Set minimum absolute alignment resolution of 0.0001 mz

  • Fix ‘peakProcess()’ not processing centroided ‘MSImagingArrays’

               Changes in version 3.8.1 (2024-12-10)

BUG FIXES

  • Fix error in ‘simulateSpectra()’ when ‘mz’ is unsorted

  • Add ‘resolution’ and ‘fmax’ to ‘simulateImage()’

CatsCradle

                    Changes in version 1.1.2
  • Function getSubsetComponents added. This is designed to dectect the components of a gene subset in the case where median complement distance detects clustering.

  • Function edgeLengthsAndCellTypePairs rewritten for faster runtime.

                      Changes in version 1.1.1
  • Default behaviour of nbhdsAsEdgesToNbhdsAsList changed to exclude self. This fixes a bug leading to inflated values of MoransI.

cBioPortalData

                   Changes in version 2.20.0

New features

  • Add copyNumberData helper function to cBioPortalData
  • Add studyId argument to the fetchData function
  • Use molecularProfiles to determine mutation or copy number molecular profile type; previously this was deduced from the data name
  • Add example for filtering discrete copy number data

Bug fixes and minor improvements

  • Caching calls removed from cBioPortalData. API requests will always be performed. cBioDataPack will continue to cache data files.
  • Filter out NULL parameters in internal .invoke_fun() API calls
  • Fix edge case in clinical data parsing when only a single file is present
  • Update long unit tests expectations to reflect current study coverage (80%)
  • Various documentation and example improvements

celda

             Changes in version 1.22.1 (2024-10-29)
  • Fixed issue with enrichR not being loaded

cfTools

                    Changes in version 1.8.0

NEW FEATURES

  • Add the PlotFractionPie() function, which generates a pie chart for a vector of cfDNA fractions.

MINOR IMPROVEMENTS

  • Updated output column names for clarity and adjusted file format for consistency across functions.

  • Suppressed non-critical TensorFlow warning messages.

ChIPpeakAnno

                   Changes in version 3.41.1
  • Update Jianhong’s email address.

ClassifyR

                   Changes in version 3.12.0

  • Metric calculation restored to permutation level by default, modifiable by parameter.

  • crissCrossValidate has TOP mode.

  • easyHard convenience function for calculating sample-specific accuracy and regressing covariates to it.

  • Parameter tuning grid no longer executed by default.

  • crossValidate’s formal parameters reduced.

cleanUpdTSeq

                   Changes in version 1.45.1
  • Update email address.

clusterProfiler

                   Changes in version 4.15.2
  • more general regular pattern to remove species suffix in KEGG pathway name (2025-02-27, Thu)

  • remove input duplicated genes in groupGO() (2024-11-29, Fri, #741)

                     Changes in version 4.15.1
  • simplify() keeps the most informative term if there exist multiple terms that meets the criteria (2024-11-29, Fri, #744)
  • add ‘RichFactor’, ‘FoldEnrichment’ and ‘zScore’ in enrichDAVID() result (2024-11-12, Tue)
  • update DAVID Web Service URL to make enrichDAVID() work properly (2024-11-09, Sat)
  • https://davidbioinformatics.nih.gov/content.jsp?file=WS.html
  • add new citation (2024-11-07, Thu)
  • https://doi.org/10.1016/j.xinn.2024.100722

ClustIRR

                   Changes in version 1.5.41

  • Function for community inspection/decoding

                     Changes in version 1.5.36

  • Two function for visualization of results: get_honeycombs and get_beta_violins

cola

                   Changes in version 2.13.1
  • register functions are put inside .onAttach()

CompoundDb

                    Changes in version 1.11

Changes in version 1.11.2

  • Import extractByIndex() from ProtGenerics.

Changes in version 1.11.1

  • Complete unit test coverage.

COTAN

                    Changes in version 2.7.5

Solved issue with use of parallelDist::parDist() by allowing a fall-back to stats::dist(). This was needed to address failures running parDist() on Linux-aarch64 machines

                    Changes in version 2.7.4

Solved bug causing errors while using torch with a CPU device

Ensure the drop out cluster from cellsUnifromClustersing() [-1] keeps its name if it has not been merged at the end of the function mergeUniformCellsClusters()

Stopped using broken BioConductor PCAtools::pca: using BioSingular::runPCA() instead

Added new utility function asClusterization() that takes any input representing a clusterization (factor, vector or data.frame) and makes it into a factor. This function is now used in all functions taking in a clusterization to standardize the given input

Added initialIteration as input parameter to clusterization functions so to avoid override of partial data when the functions are being restarted

                    Changes in version 2.7.3

Added new function clusterGeneContingencyTables(): it returns observed and expected contingency tables for a given gene and group of cells (cluster)

                    Changes in version 2.7.2

Added possibility to specify genes’ selection method used in the cellsUniformClustering() function

Improved “AdvancedGDIUniformityCheck” by adding a new check about 99% quantile

Solved issue in clustersMarkersHeatmapPlot(): now passing in a genes not in the data-set will result in a corresponding gray column instead of an error

Added possibility to specify clean() thresholds in the functions proceedToCoex() and automaticCOTANObjectCreation()

                    Changes in version 2.7.1

Improved function clustersMarkersHeatmapPlot(): now its shows a column for each marker gene and the shown content is more expressive

Marked the function clustersDeltaExpression() as legacy: it has been replaced with the function DEAOnClusters() in the package

Fixed minor bug in class AdvancedGDIUniformityCheck regarding third check: was testing third highest GDI value instead of second

CRISPRball

                     Changes in version 1.4
  • Bug Fixes:
    1. plot_rank(): Fixed silent bug with h.id suffix being the same as plot_volcano().

CytoMDS

                     Changes in version 1.3

CytoMDS 1.3.7

  • changed package citation (and in README.md) to peer reviewed journal article

CytoMDS 1.3.6

  • ggplotMarginalDensities(): corrected a bug when channels were specified as marker names.

CytoMDS 1.3.5

  • removed contraint (max = 3) on nb of plotly tool_tips variables (pDataForAdditionalLabelling)

CytoMDS 1.3.4

  • corrected plotly tool_tips (pDataForAdditionalLabelling)

CytoMDS 1.3.3

  • DistSum class to store distance matrices computed as the sum of marker contributions
  • ggplotDistFeatureImportance() now can be used to create a stacked bar ggplot object, displaying feature importance in a distance matrix (extracted from a DistSum object)

CytoMDS 1.3.2

  • added pointSize argument to ggplotSampleMDS()

CytoMDS 1.3.1

  • corrected bug with nPoints() method of MDS class, due to slightly modified behaviour of dist S3 class in R4.5.

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
                   Changes in version 1.45.1
  • update email address.

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”)

DegCre

                    Changes in version 1.3.0

NEW FEATURES

  • Again updated collapseDegCreToGene to run much faster. No longer accepts a useParallel argument. Does not use BiocParallel.

BUG FIXES

  • Fixed bug in convDegCreResListToCreGeneScoreGR that called a deprecated function.

DelayedArray

                   Changes in version 0.34.0

NEW FEATURES

  • Implement delayed paste2() for DelayedArray objects. This makes BiocGenerics::add_prefix() and BiocGenerics::add_suffix() work out-of-the box on DelayedArray objects.

SIGNIFICANT USER-VISIBLE CHANGES

  • Binary operations between a DelayedArray object and an array now raise an error. This is temporary and only to prevent users from trying to use a tile object (new in S4Arrays 1.7.3) on the left or right side of the operation, and get the wrong result.

  • Revisit implementation of the path() getter (and setter) for DelayedOp. The new implementation is recursive so will acknowledge path() methods defined for custom DelayedOp derivatives like the path() getter defined for ReloadedArraySeed objects in the alabaster.matrix package.

DEPRECATED AND DEFUNCT

  • SparseArraySeed objects, OLD_extract_sparse_array(), and read_sparse_block() are now defunct after being deprecated in BioC 3.20.

  • Get rid of previously defunct stuff. This is:

    • blockGrid(): replaced with defaultAutoGrid()
    • rowGrid(): replaced with rowAutoGrid()
    • colGrid(): replaced with colAutoGrid()
    • multGrids(): replaced with defaultMultAutoGrids()
    • viewportApply(): replaced with gridApply()
    • viewportReduce(): replaced with gridReduce()
    • getRealizationBackend(): replaced with getAutoRealizationBackend()
    • setRealizationBackend(): replaced with setAutoRealizationBackend() All these functions went defunct 2.5 years ago in BioC 3.15.

DESeq2

                   Changes in version 1.47.4
  • Adding pasilla extdata to DESeq2 package for build stability.

DESpace

                   Changes in version 1.99.1

  • add detection of differential spatial patterns (DSP) across conditions

  • rename functions for consistency

  • enable FeaturePlot for non-Visium/ST data

dominoSignal

                    Changes in version 1.0.5

  • circos_ligand_receptor will not fail in cases where the rl_map of a domino objects includes ligands for a receptor where the ligands are not present in the expression matrix. A message is returned if ligands from the rl_map had to be excluded from the plot

                      Changes in version 1.0.4

  • refactorization of circos_ligand_receptor function to remove use of grepl-based regular expressions to reformat cell and molecule names from a domino object into a data frame for plotting a receptor circos plot. Component functions for creating the data frame of ligand expression centered on a single receptor and to render this data frame as a circos plot are now included in the package as “obtain_circos_expression” and “render_circos_ligand_receptor”, respectively.

                      Changes in version 1.0.3

  • Added functions for calculation of mean gene expression among components of a complex using purrr functions

                      Changes in version 1.0.2

Pkgdown Site Customization Scripts

  • Restored _pkgdown.yml and index scripts that specify site building parameters for https://FertigLab.github.io/dominoSignal to improve formatting.

                      Changes in version 1.0.1

Receptor Complex Bugfix

  • Resolved issue where if create_domino was run with complexes=TRUE and no complexes were found to have active signaling, the full signaling matrix would be replaced by a NULL value.

GitHub Actions

  • Restoration of .github/workflows scripts for automatic build checks.

dreamlet

                    Changes in version 1.4.1
  • March 25, 2025
  • improve checking for sample_id and cluster_id in aggregateToPseudoBulk()

DropletUtils

                   Changes in version 1.28.0

  • Use a more stable algorithm for identifying the knee point in barcodeRanks(). The new algorithm is based on maximizing the distance from a line between the plateau and the inflection point. Previously, we tried to minimize the signed curvature but this was susceptible to many local minima due to the instability of the empirical second derivative, even after smoothing.

  • Set alpha=Inf as the default for testEmptyDrops(). This is motivated by the realization that an underestimated alpha can still yield anticonservative p-values and is not universally safer than alpha=Inf. Defaulting alpha=Inf is preferable as it is at least correct in the expected case of multinomial sampling.

DuplexDiscovereR

                    Changes in version 1.1.2
  • Date: 2025-03-12

  • Removed BiocCheck files

                      Changes in version 1.1.1
  • Date: 2024-12-30
  • Added added raw abundance values and duplex counts for 2x2 contingency table to the p-value calculation output

EBSeq

                    Changes in version 2.5.2
  • Using c++14 for the updated [BH] (https://cran.r-project.org/web/packages/BH/index.html) dependency, and restrict BH version <= 1.87.0-1 to prevent higher version C++ requirement in the future

edgeR

             Changes in version 4.6.0 (2025-04-16)

  • edgeR now depends on limma >= 3.63.6.

  • New diffSplice() method for DGEGLM objects. The output object has the same format as that from the diffSplice() method in the limma package for MArrayLM objects. The new method is intended to replace diffSpliceDGE(), although the latter is kept for the current release for backward compatibility. The new diffSplice() method is slightly slower than diffSpliceDGE(), but has improved power and receiver operating curve while still controlling the FDR correctly.

  • Corrections to diffSpliceDGE() so that it provides more rigorous control of the FDR. The numerator degrees of freedom used for the gene-level tests is increased by 1.

  • getOffset() now gives an error if the data object doesn’t contain library sizes.

  • The entries in the package DESCRIPTION file have been revised and reformated.

enrichplot

                   Changes in version 1.27.5

  • able to scale pie size for ‘compareClusterResult’ (2025-03-11, Tue, #308, #311)

                     Changes in version 1.27.4
  • adjust pie size and category label position in cnetplot() (2025-01-08, Wed, #306)

  • clean up code (2024-12-20, Fri)

                     Changes in version 1.27.3
  • scale pies and add pie legend in emapplot() (2024-12-12, Thu, #304)

  • a safe way to extract gene sets in ridgeplot() (2024-12-12, Thu, #303)

                     Changes in version 1.27.2
  • emapplot() now allows passing color to a specific color, e.g., color = “black” (2024-11-29, Fri, #300)
  • bug fixed in emapplot()
  • size_category now works for pie node (2024-11-29, Fri, #301)
  • legend of term nodes will be retained when group = TRUE (2024-11-29, Fri, #300)
  • supports passing ID to ‘showCategory’ in ridgeplot() (2024-11-06, Wed, #295)
  • enhancement of cnetplot() (2024-11-06, Wed)
  • ‘node_label’ can be a vector of selected items/genes to specify the items to be displayed (#293)
  • ‘node_label’ can be ‘exclusive’ to label genes that are uniquely belongs to categories (#253)
  • ‘node_label’ can be ‘share’ to label genes that are share between categories (#253)
  • ‘node_label’ can be, e.g. ‘> 1’ or ‘< 1’, to label genes that have log2FC values larger or smaller than the threshold (#253)
  • supports using ggtangle::geom_cnet_label() to label items/genes in independent layer (#194, #266, #267)

  • fixed ridgeplot() when selecting a specific gene set and plotting non-core genes (2024-11-06, Wed, #298)

                     Changes in version 1.27.1

  • add ‘ID’ parameter in goplot() (2024-10-30, Wed)

    https://github.com/YuLab-SMU/enrichplot/issues/292#issuecomment-2445788948

epialleleR

             Changes in version 1.15.3 (2025-03-05)

  • test coverage for namespaces

  • new ref

               Changes in version 1.15.1 (2024-11-16)

  • can override alignment endness when loading BAM

EpiCompare

                   Changes in version 1.11.3

  • Update minimum version for dependency IRanges. See issue #155.

                     Changes in version 1.11.1

Bug Fixes

  • prepare_output_build
  • Fix support for mouse genome builds (mm9 and mm10).

Documentation

  • Epicompare.Rmd
  • Mention support for mouse genome builds.

EpiDISH

                   Changes in version 2.23.1
  • Added unified lifecourse 19 immune cell-type reference matrix for 450k and EPIC arrays.

escape

                    Changes in version 2.2.4

UNDERLYING CHANGES

  • moved dependency from msigdbr to msigdb
  • getGeneSets() now locally caches the gene sets to improve speed of repeated use

  • getGeneSets() now only supports Mouse or Human

                      Changes in version 2.2.3

UNDERLYING CHANGES

  • fixed handling of groups parameter and data splitting in escape.matrix()

  • improved efficiency of internal .split_data.matrix()

                      Changes in version 2.2.2

UNDERLYING CHANGES

  • fix performNormalization() conditional statements

  • fix performNormalization() rescaling for per gene set calculations

                      Changes in version 2.2.1

EWCE

                   Changes in version 1.15.1

Bug fixes

  • Remove print statements, clean up CTD creation steps.

extraChIPs

                   Changes in version 1.11.2
  • Changed handling of arguments in plotting functions, setting NULL as the primary default value

fenr

                    Changes in version 1.4.2

  • Added evidence code column to GO-term mapping table. It can be used to filter mapping based on their quality. See https://geneontology.org/docs/guide-go-evidence-codes for explanation.

                      Changes in version 1.4.1

  • Attempted to fix a bizarre error message on Bioconductor’s test machines with older version of MacOS. Windows and Linux are not affected; my laptop running Sequoia 5.2 does not show show errors. I suspect a memory leak in older systems. The error vector memory limit of 64.0 Gb reached, see mem.maxVSize() happened in the function parse_kegg_genes(), a flat-file parser for KEGG. It occurred around the call tidyr::separate(), which I replaced with an alternative approach. Will see if the error is fixed.

fgsea

                   Changes in version 1.33.3
  • update code for using msigdbr in geseca vignette

flowcatchR

                   Changes in version 1.42.0

Other notes

  • Some changes in the source of the documentation, providing anchors to all function calls. This avoids the new note in R CMD check in the new major release

fmrs

                    Changes in version 2.0.1

IMPROVEMENTS SINCE LAST RELEASE

  • Non-mixture of regression models are now added to the package.

BUG FIXES

  • Several bugs are fixed.

                      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 1.15.1
  • Fix bugs in vignettes

gDNAx

             Changes in version 1.6.0 (2025-04-14)

USER VISIBLE CHANGES

  • Handling of metadata from non-model organisms has been improved. Thanks to discussions on the support site (https://support.bioconductor.org/p/9160897/) and GitHub (https://github.com/rcastelo/gDNAx/issues/5).

  • Added more documentation to the output of the ‘getDx()’ method.

gDRcore

           Changes in version 2025-03-31 (2025-03-31)

  • extend the logic of functions for getting annotation from dt to fill missing cols with unknown

             Changes in version 2025-03-10 (2025-03-10)

  • move map_conc_to_standardized_conc to gDRutils package

             Changes in version 2025-03-05 (2025-03-05)

  • update assay names for combo data in get_assays_per_pipeline_step function

             Changes in version 2025-01-13 (2025-01-13)

  • switch to gDRutils::remove_drug_batch function

             Changes in version 2024-12-18 (2024-12-18)

  • fix melt error after changed intersect behaviour

             Changes in version 2024-11-15 (2024-11-15)

  • fix melt in annotation function to fix Bioc error

gDRimport

           Changes in version 2025-04-10 (2025-04-10)

  • replace with_mock with with_mocked_bindings

             Changes in version 2025-03-26 (2025-03-26)

  • unify support for using OncotreeLineage for PRISM level 5 and level 6

             Changes in version 2025-03-12 (2025-03-12)

  • add support for using OncotreeLineage as a tissue annotation if available in PRISM data

             Changes in version 2025-02-18 (2025-02-18)

  • update extracting Tissue information for cell lines in PRISM data

             Changes in version 2025-02-07 (2025-02-07)

  • extract Tissue information for cell lines in PRISM data

             Changes in version 2025-02-04 (2025-02-04)

  • update error messages, to make them less confusing

             Changes in version 2025-01-11 (2025-01-11)

  • take into account run in public PRISM data

             Changes in version 2024-12-09 (2024-12-09)

  • support Duration in old private PRISM data format

             Changes in version 2024-12-04 (2024-12-04)

  • support old private PRISM data format

             Changes in version 2024-11-06 (2024-11-06)

  • fix invalid moa for PRISM data

             Changes in version 2024-11-05 (2024-11-05)

  • synchronize Bioconductor and GitHub versioning

gDRstyle

           Changes in version 2025-02-11 (2025-02-11)

  • make different default lintr config for different versions of lintr

             Changes in version 2025-02-08 (2025-02-08)

  • switch off return_linter in default lintr config

             Changes in version 2025-02-04 (2025-02-04)

  • move BiocStyle to Depends

             Changes in version 2025-01-20 (2025-01-20)

  • update notes.json

             Changes in version 2024-11-05 (2024-11-05)

  • synchronize Bioconductor and GitHub versioning

gDRutils

           Changes in version 2025-03-26 (2025-03-26)

  • fix default parameter in get_settings_from_json

             Changes in version 2025-03-19 (2025-03-19)

  • add get_gDR_session_info function

             Changes in version 2025-03-18 (2025-03-18)

  • move split_big_table_for_xlsx from gDRsearch2 package

             Changes in version 2025-03-12 (2025-03-12)

  • improve logic in get_assay_req_uniq_cols

             Changes in version 2025-03-07 (2025-03-07)
  • add support for combination experiment in cap_assay_infinities

  • move map_conc_to_standardized_conc from gDRcore package

             Changes in version 2025-02-21 (2025-02-21)

  • refactor average_biological_replicates

             Changes in version 2025-02-14 (2025-02-14)

  • update default value of capping_fold param in cap_assay_infinities

             Changes in version 2025-02-05 (2025-02-05)

  • add support for dropping masked values in the assay data

             Changes in version 2025-02-03 (2025-02-03)

  • keep ‘replicate’ column as additional perturbation in get_additional_variables

             Changes in version 2025-01-30 (2025-01-30)

  • add support for unifying metadata in convert_se_assay_to_dt function

             Changes in version 2025-01-24 (2025-01-24)

  • add cap_assay_infinities

             Changes in version 2025-01-13 (2025-01-13)

  • refactor remove_drug_batch

             Changes in version 2024-12-10 (2024-12-10)

  • make split_SE_components working correctly for sa assay data, modified with avearge_biological_duplicates

             Changes in version 2024-12-09 (2024-12-09)

  • minor improvement in the logic of average_biological_replicates (new blacklisted column)

             Changes in version 2024-12-02 (2024-12-02)

  • refactor set_unique_* functions

             Changes in version 2024-11-05 (2024-11-05)

  • add get_env_var helper

  • synchronize Bioconductor and GitHub versioning

gdsfmt

                   Changes in version 1.44.0

UTILITIES

  • fix the C++ error with Apple clang version 17: no ‘std::basic_string' & 'std::basic_string'

                     Changes in version 1.42.2

UTILITIES

  • tweak the C Macro to support Linux MUSL

  • fix according to the C compiler C23

gemma.R

                    Changes in version 4.0.0
  • get_annotation_children and get_annotation_parents are added. get_child_terms is deprecated in favor of get_annotation_children

GeneNetworkBuilder

                   Changes in version 1.49.2

  • Add warning message if there is no stringApp installed.

                     Changes in version 1.49.1

  • Update email address.

GENESIS

                   Changes in version 2.37.1
  • Add option “imputed” to admixMap to allow testing imputed dosages.

GeneTonic

                    Changes in version 3.2.0

Bug fixes

  • The tooltip functionality in visualizing the ggs_graph() output now handles correctly the text for the geneset description. Thanks to @thomas-keller for spotting this and for the fix!

Other notes

  • gene_plot() defaults now to NULL in the intgroup parameter, which translates into using the first colData item

GenomAutomorphism

                    Changes in version 1.8.1
  • Add new a new function: ‘automorphism_prob’, which applies a Dirichlet-Multinomial Modelling (in a Bayesian framework) to compute the posterior probability of each type of mutational event.

GenomeInfoDb

                   Changes in version 1.44.0

NEW FEATURES

  • Register the following NCBI assemblies:
    • GAculeatus_UGA_version5 (Stickleback)
    • GadMor_May2010 and gadMor3.0 (Atlantic cod)
    • Orenil1.1 and O_niloticus_UMD_NMBU (Nile tilapia)
    • CriGri_1.0, C_griseus_v1.0, and CriGri-PICRH-1.0 (Chinese hamster)
  • Register the following UCSC genomes:
    • gadMor1 (Atlantic cod), based on NCBI assembly GadMor_May2010
    • oreNil2 (Nile tilapia), based on NCBI assembly Orenil1.1
    • criGri1 (Chinese hamster), based on NCBI assembly C_griseus_v1.0

SIGNIFICANT USER-VISIBLE CHANGES

  • Use slightly better heuristic in getChromInfoFromNCBI() for guessing the circular sequences of non-registered assemblies.

BUG FIXES

  • Fix getChromInfoFromNCBI(“panpan1.1”). See commit 3be5818.

GenomicAlignments

                   Changes in version 1.44.0
  • No changes in this version.

GenomicDataCommons

                   Changes in version 1.32.0

Bug fixes and minor improvements

  • Minor updates to unit tests and GitHub Actions

GenomicFeatures

                   Changes in version 1.60.0

DEPRECATED AND DEFUNCT

  • Formally deprecate all the functions that went to txdbmaker in BioC 3.19.

GenomicInteractionNodes

                   Changes in version 1.11.3

BUG FIXES

  • Fix multiple typos.

                     Changes in version 1.11.2

BUG FIXES

  • Fix the error “invalid ‘scipen’”.

                     Changes in version 1.11.1

BUG FIXES

  • Update email address.

GenomicPlot

                    Changes in version 1.5.3

  • Modified handle_bed to allow skipping of first n rows

                      Changes in version 1.5.2

  • Modified draw_matrix_heatmap to handle momogeneous matrix

                      Changes in version 1.5.1

  • Modified draw_matrix_heatmap to allow it to handle extreme cases

GenomicRanges

                   Changes in version 1.60.0
  • No changes in this version.

geomeTriD

                   Changes in version 1.1.11

NEW FEATURES

  • Add createTADGeometries function.

                     Changes in version 1.1.10

NEW FEATURES

  • Add pointCluster.

                      Changes in version 1.1.9

BUG FIXES

  • Fix multiple typos.

                      Changes in version 1.1.8

BUG FIXES

  • Fix the issues “Uncaught SyntaxError: Expected ‘,’ or ‘]’ after array element in JSON” if data.frame is too big.

                      Changes in version 1.1.7

BUG FIXES

  • Fix the issues of measurment marker do not rotate and unexpected resize window when export.

                      Changes in version 1.1.6

BUG FIXES

  • Export pdf with visible layers only.

                      Changes in version 1.1.5

NEW FEATURES

  • Add pdf exporter.

                      Changes in version 1.1.4

BUG FIXES

  • Fix the input check issue in kabsch.

                      Changes in version 1.1.3

BUG FIXES

  • Update email address.

                      Changes in version 1.1.2

NEW FEATURES

  • Add resolution for view3dStructure.

                      Changes in version 1.1.1

NEW FEATURES

  • Add autocomplete input for search key words.

GEOquery

             Changes in version 2.99.0 (2024-10-01)

New Features

  • RNAseq data support for GEOquery. Now you can use RNASeq quantification data prepared by NCBI.
  • Basic search in GEO database. Now you can search for datasets in GEO database using GEOquery.
  • browseGEO() function to open a web browser with a GEO accession.

Breaking changes

  • getGEO() now returns a list of SummarizedExperiment objects. This is a breaking change from previous versions of GEOquery. If you are using GEOquery in a script, you will need to update your code to reflect this change.

Bug Fixes or Improvements

Not an exhaustive list, but some highlights:

  • Using httr2 instead of curl for better control over HTTP requests.
  • Removed dead gunzip code.

getDEE2

                   Changes in version 1.17.3

  • Better handling of exact query matches to bundle names.

                     Changes in version 1.17.1

  • Added support for O sativa (rice) and Z mays (corn) in the DEE2 database. Thanks to Dr Wen-Dar Lin, Bioinformatician at IPMB, Academia Sinica, Taiwan, for contributing these data.

ggseqalign

                    Changes in version 1.1.2

  • Updated installation instructions in Vignette to reflect Bioconductor release with correct version number

                      Changes in version 1.1.0

  • Automatic bump from Bioconductor

                      Changes in version 1.0.2

  • Updated installation instructions in Vignette to reflect Bioconductor release

                      Changes in version 1.0.1

  • Updated installation instructions in README to reflect Bioconductor release

ginmappeR

                    Changes in version 1.2.3

ENHANCEMENT

  • .testEquals function revised.

                      Changes in version 1.2.2

ENHANCEMENT

  • UniProt similar genes tests revised for macOS platforms.

                      Changes in version 1.2.1

ENHANCEMENT

  • KEGG to NCBI and UniProt similar genes tests revised.

gINTomics

                    Changes in version 1.4.0

  • New class comparison analysis. Now the package run a single analysis for all classes together and then highlights the results for differentially expressed genes for all the available comparisons.

  • New Differentially Methylated genes analysis available.

  • New Differential Copy Number Variations analysis available.

  • Added DEGs section in the shiny app.

  • Added expression insights sections in the shiny app.

  • General improvements.

glmGamPoi

              Changes in version 1.19 (2024-11-26)

  • glmGamPoi is using the new tatami library instead of the old beachmat interface. These libraries helped to work with different kind of matrices (dense, HDF5-backed). One important change is that glmGamPoi now requires C++17 (instead of C++14). (PR#66,thanks Aaron Lun)

  • The input data can be sparse! Building on top of tatami allows me to support arbitrary matrix types such as sparse matrices and DelayedArrays.

  • Fix bug regarding matrix columns in pseudobulk (https://github.com/const-ae/lemur/issues/20).

  • Add work-around for https://github.com/Bioconductor/DelayedArray/issues/123

GNOSIS

             Changes in version 1.99.0 (2023-09-04)

  • Made the following significant changes o added functionality to select and upload cBioPortal study o deprecated ability to save R script with executed code

  • Submitted to Bioconductor

goSorensen

                   Changes in version 1.10.0

In this updated version, unless the user specifies otherwise in the onlyEnriched argument of the enrichedIn function, the enrichment matrix of GO terms includes only those terms that are enriched in at least one of the lists being compared, excluding all terms that are not enriched in any of the lists. This optimization significantly reduces computation times for enrichment analysis compared to previous versions, such as when generating enrichment contingency tables using buildEnrichTable.

Additionally, with the latest versions of Bioconductor and its updated packages, we have revised the naming conventions and outputs for results obtained from the primary goSorensen functions. These changes are summarized in two new bullet points, offering clearer guidance and improved usability for package users compared to earlier versions.

graphite

             Changes in version 1.53.1 (2024-04-14)
  • Updated all pathway data.

GSVA

                    Changes in version 2.20

USER VISIBLE CHANGES

  • When the input expression data is provided as either a ‘SummarizedExperiment’, ‘SingleCellExperiment’ or a ‘SpatialExperiment’ object, the default assay is now either one called ‘logcounts’ or the first one, otherwise.

  • Added a method called ‘spatCor()’ to efficiently compute spatial autocorrelation using Moran’s I statistic for an input ‘SpatialExperiment’ object, using an inverse squared distance weight matrix as default, or an inverse distance weight matrix as an alternative. It also tests for spatial autocorrelation assuming normality. This functionality is added to help detecting autocorrelated gene sets using GSVA enrichment scores.

  • After one cycle of deprecation and two cycles of being defunct, the classical non-object-oriented way of calling the function ‘gsva()’ has been completely removed. Now ‘gsva()’ can only be used by constructing first a parameter object.

  • Fixed URLs in vignette and DOI refs in documentation.

  • The vignette has been updated with a new section illustrating how to import gene sets from GMT files with the function ‘readGMT()’ and the section on “Differential expression at pathway level” has been updated using the bulk RNA-seq data from Costa et. al (2021).

BUG FIXES

  • Bugfix in gsvaEnrichment() when input data contains missing values.

  • Bugfix in checking and detecting missing values in input expression data.

  • Bugfix in the PLAGE method when using the argument BPPARAM with a value other than Serial

Param(). It resolves issue #220

  • Bugfix when tau is not double for the GSVA method.

  • Bugfix in the C code to avoid potential memory leaks.

HDF5Array

                   Changes in version 1.36.0

NEW FEATURES

  • The package now has a vignette that discusses/compares performance of various HDF5-based representations in the context of single cell analysis.

SIGNIFICANT USER-VISIBLE CHANGES

  • h5mread() and other low-level HDF5 manipulation functions have moved from the HDF5Array package to the new h5mread package and the former now depends on the latter.

DEPRECATED AND DEFUNCT

  • All the OLD_extract_sparse_array() and read_sparse_block() methods are gone (the corresponding generics went defunct in DelayedArray 0.33.1).

BUG FIXES

  • Make sure writeTENxMatrix() can handle a matrix-like object with more than 2^31 - 1 nonzero values.

HoloFoodR

                    Changes in version 1.1.1

Date: 2025-04-03

  • Improved MetaboLights support

                      Changes in version 1.1.0

Date: 2024-10-24

  • Add addMGnify function

HuBMAPR

                    Changes in version 1.0.8

  • Update the vignette plots by adding more disguishable colors

                      Changes in version 1.0.7

  • Error check

                      Changes in version 1.0.6

  • Updated NEW.md

                      Changes in version 1.0.5
  • Updated dataset_metadata() function to accommodate with API changes
  • Reformatted vignette with with more technical details based on comments

  • Added summary lists in README

                      Changes in version 1.0.4
  • Updated dataset_metadata() function to accommodate with API changes
  • Reformatted vignette with with more technical details based on comments

  • Added summary lists in README

  • Updated functions to accommodate with API changes

HubPub

             Changes in version 1.15.3 (2024-01-21)

  • Update CreateAHubPackageVignette to include R package code for data upload

               Changes in version 1.15.1 (2024-01-13)

  • Update CreateAHubPackageVignette to use S3 instructions for data upload

ideal

                    Changes in version 2.2.0

Other notes

  • Some changes in the source of the documentation, providing anchors to all function calls. This avoids the new note in R CMD check in the new major release

immApex

                    Changes in version 1.0.5

UNDERLYING CHANGES

  • getIMGT() checks for availability of IMGT website
  • Expanded Unit Tests

  • Unit Tests and Vignette now evaluate for proper python installation overall

                      Changes in version 1.0.4

UNDERLYING CHANGES

  • Optional testthat variationalSequences() evaulate presence of Keras

                      Changes in version 1.0.3

UNDERLYING CHANGES

  • Drop evaluation of variationalSequences() example

                      Changes in version 1.0.2

UNDERLYING CHANGES

  • Vignette includes eval of keras installation for certain chunks

                      Changes in version 1.0.1

UNDERLYING CHANGES

  • Fix issue with optimizer call in variationalSequences()
  • Move package to keras3
  • Version Bump to be consistent with Bioconductor release

immunoClust

                   Changes in version 1.39.4
  • -CHANGES

    • sanitize parameter desciption in immunoMeta-object

                    Changes in version 1.39.2-3
  • CHANGES

    • fixes BioC 3.21 compiler errors

                     Changes in version 1.39.1
  • CHANGES
    • in subset.immunoClust keep NAs in label of subset-object
    • respect already transformed FCS-data in Default_Scales

InPAS

                   Changes in version 2.15.2

  • Update email address.

                     Changes in version 2.15.1

  • Add citation.

IRanges

                   Changes in version 2.42.0

SIGNIFICANT USER-VISIBLE CHANGES

  • New implementations of the viewMins(), viewMaxs(), viewSums(), viewMeans(), viewWhichMins(), viewWhichMaxs(), viewRangeMins(), and viewRangeMaxs() methods for RleViews objects. This is a complete rewrite (including of the C code behind these methods) that addresses many long-standing (and unnoticed-for-years) bugs in the previous implementation. This new implementation can also be significantly faster than the previous one e.g. 5x faster or more for RleViews objects with millions of views.

BUG FIXES

  • Fix multiple bugs in viewMins(), viewMaxs(), viewSums(), viewMeans(), viewWhichMins(), viewWhichMaxs(), viewRangeMins(), and viewRangeMaxs() methods for RleViews objects. See above for the details.

  • Fix bug in disjointBins() method for IntegerRanges derivatives when the input object has names and is not sorted. See https://github.com/Bioconductor/IRanges/issues/54 for the details.

iSEE

                   Changes in version 2.19.4

  • Added a parameter to control the title displayed in the browser tab, currently defaulting to “iSEE”. Thanks to @RiboRings for the implementation!

                     Changes in version 2.19.3

  • Added an option to have no legend shown in the dotplot panel class

                     Changes in version 2.19.1

  • Changed the processing of the title for the app - if provided explicitly, now it can also correctly handle HTML content tags and more. Thanks to @RiboRings for spotting this, resolving #681

iSEEtree

                     Changes in version 1.1

  • Updated .multiSelectionResponsive

  • Conformed to iSEE v2.19.2

  • Created TreePlot family

  • Added typical tree operations

  • Created GraphPlot family

  • Added ScreePlot panel

  • Added PrevalencePlot panel

Lheuristic

                    Changes in version 1.0.0

  • Package added to Bioconductor

  • Bioc-submission branch merged with master

limma

             Changes in version 3.64.0 (2025-04-16)

  • In topSplice(), the default for test is now “F” instead of “simes”.

  • diffSplice() is now an S3 generic function with a method for MArrayLM objects.

  • New argument legacy for diffSplice().

  • diffSplice() now adjusts transcript-level p-values using the full Simes method, instead of a modified Simes method leaving out the largest p-value for each gene that has been used until now. This will cause the Simes p-values returned by diffSplice() to be slightly more conservative than before.

  • diffSplice() now returns Bonferroni adjusted p-values as an alternative to Simes method.

  • The gene.genes data.frame returned by diffSplice() now has row names set to the gene IDs. Previously the last exon ID for each gene was used.

  • diffSplice() now allows for exons with df.residual=0 and sigma=NA.

  • Bug fix to diffSplice() when fitFDistUnequalDF1() was called with robust=TRUE, i.e., whenever robust=TRUE and the number of transcripts differs between genes.

  • Bug fix to genewise variance pooling in diffSplice() when the residual df are unequal. Previously the exon-wise variances were not weighted by df when pooling.

  • New argument directional for camera() and cameraPR().

  • vooma() now allows missing values in both y and predictor, provided there are no entirely missing rows and provided all non-NA y values have a non-NA predictor.

  • voomaLmFit() now allows missing values in y and predictor, provided there are no entirely missing rows and provided all non-NA y values have a non-NA predictor.

  • voomaLmFit() now allows predictor to be either a matrix or a column vector with genewise values.

  • Edit voomaLmFit() help page. Add Li (2024) PhD Thesis as reference.

maaslin3

                    Changes in version 3.0.1

  • Changed data augmentation for logistic models

  • Replaced iterative renormalization with median comparisons

  • Replaced group, OMP, and GOMP models with contrast tests and ANOVA-style comparisons

                      Changes in version 3.0.0

  • Updated dependencies

  • Modularized previous code

  • Added prevalence/logistic models

  • Added data augmentation for logistic models

  • Added iterative renormalization for compositionally

  • Added spike-in references for compositionally

  • Added group, OMP, and GOMP models

MassSpecWavelet

             Changes in version 1.73.1 (2024-12-18)
  • Fix off-by-one error. Thanks to Aixiang Jiang, Ivan Krylov, Lluís Revilla, Duncan Murdoch and Vincent Carey for reporting, suggesting a fix and reaching out.

matter

                    Changes in version 2.9.1

BUG FIXES

  • Change C-level ‘Free()’ calls to ‘R_Free()’

MetaboAnnotation

                    Changes in version 1.11

Changes in 1.11.1

  • Fix reporting of matched peaks with MatchForwardReverseParam and gnps-matching/similarity calculation (issue #119).

methyLImp2

             Changes in version 1.3.1 (2025-02-04)
  • Fixing wrong counter in the loop.

methylKit

                   Changes in version 1.33.3

IMPROVEMENTS AND BUG FIXES

  • remove import of “key<-“ function deprecated since data.table 1.17.0

  • update makeMethTabix call to remove temporary file after processing

  • refactor destrand function to handle non-base resolutions and streamline file cleanup

                     Changes in version 1.33.2

IMPROVEMENTS AND BUG FIXES

  • processBismarkAln: fix cigar buffer storage issue which led to faulty methylation calls (#334)

  • remove zlibbioc dependency, zlibbioc is now deprecated in Bioc 3.21 and will be removed in Bioc 3.22

                     Changes in version 1.33.1

IMPROVEMENTS AND BUG FIXES

  • bedgraph: fix bedgraph error due to NA handling in meth.diff export (#331)

mia

                    Changes in version 1.15

  • subsetBy*: added update.tree argument

  • agglomerateBy*: Add na.rm option for excluding NA counts

  • Added getPERMANOVA and addPERMANOVA functions to calculate PERMANOVA

  • update.tree = TRUE by default

  • Add functions for classifying taxa based on their average abundance

  • Add addPrevalence function that adds results of getPrevalence to rowData

  • Added support for dimred to getCrossAssociation

  • Add wrapper for PhILR transformation

  • Support rarefaction when applying unifrac

  • Added getMDS and addMDS: wrappers for scater::calculateMDS and scater::runMDS

  • Fix tree merging and agglomeration

  • getReducedDimAttribute: function for fetching elements from attributes of reducedDim

  • Improve decontam functions

  • Support precalculated dissimilarity matrix in dbRDA

  • Calculate standard, binary Jaccard index by default

miaViz

                    Changes in version 1.15

  • plotAbundance: Improved visualization of sample metadata

  • plotScree: Method for creating scree plots

  • plotRDA: Now it is possible to add only specified vectors

  • plotMediation: Method to visualise results of mediation analysis

  • plotRDA: Fix error that occurred when variable names were similar

  • Added plotHistogram

  • Added plotBarplot

MIRit

                    Changes in version 1.3.1

Now it is possible to use a local copy of miRTarBase with the getTargets() function.

mitch

                   Changes in version 1.19.4

  • New networkplot visualisation has been added to help interpret enrichment results.

                     Changes in version 1.19.3

  • Fixed a breaking bug in mitch_plots() for 2D analysis.

MLP

                   Changes in version 1.55.1

  • addGeneSetDescription: fix issue KEGG

  • doc: remove description-like items in itemize (R-devel 11/10/2023)

monaLisa

                   Changes in version 1.13.3
  • switched to ggplot2 with all plotting functions (except plotMotifHeatmaps that is still based on ComplexHeatmaps)
  • new arguments introduced in plotStabilityPaths() to allow for labels to be shown at the end of the stability paths if desired
  • changed some argument names in plotStabilityPaths() and plotStabilityPaths(). See the help pages of these function for more details
  • updated the stability selection vignette to showcase labeling predictors

  • exposed glmnet arguments in randLassoStabSel()

                     Changes in version 1.13.2
  • minor fix to ensure that heatmap bin legends are ordered in the same way as the heatmap columns

Moonlight2R

                    Changes in version 1.5.5

Summary

  • fixed mistake in the documentation of the TFinfluence function

                      Changes in version 1.5.4

Summary

  • added missing documentation file

                      Changes in version 1.5.3

Summary

  • Filter only missense mutations of MAF in TFinfluence.
  • Switched to RaSp/FoldX consensus as a default of MAVISp in TFinfluence.

  • Corrected the code of ‘mutation_available’ column of TFinfluence output to correctly check the presence of the mutation in MAVISp data.

                      Changes in version 1.5.2

Summary

  • Added additional columns in TFinfluence output that describe the availabilty of the TF and its mutation in MAVISp

                      Changes in version 1.5.1

Summary

  • Added TFinfluence function, that implements a secondary layer that checks the influence of destabilizing mutations on transcription factors as mechanistic explanation for expression changes

                      Changes in version 1.5.0

Summary

  • version bump due to release of Bioconductor 3.20

mosdef

                    Changes in version 1.4.0
  • gene_plot() defaults now to NULL in the intgroup parameter, which translates into using the first colData item

Motif2Site

                   Changes in version 1.11.1
  • Address the Error in Bioconductor build
  • Move the source github from Bioinference to fls-bioinformatics-core

motifStack

                   Changes in version 1.51.1
  • Update email address.

motifTestR

                    Changes in version 1.3.5

  • Introduced prior counts for enrichment testing

                      Changes in version 1.3.3

  • Added simSeq for generating random sequences

MPAC

                    Changes in version 1.1.6
  • updated pseudocode in vignettes
  • added new functions
  • pltConMtf(): to plot consensus pathway submodules
  • pltMtfPrtIPL(): to plot a heatmap of IPLs on proteins from consensus pathway submodules

  • pltSttKM(): to plot Kaplan-Meier curve for patient samples stratified by given protein(s)’ pathway states

                      Changes in version 1.1.5

  • use ‘Multi-omic Pathway Analysis of Cells’ for MPAC

                      Changes in version 1.1.4

  • updated text in DESCRIPTION

                      Changes in version 1.1.3
  • Vignettes
  • added examples on pltOvrHm()
  • added pseudocode for MPAC

  • changed MPAC’s full name

                      Changes in version 1.1.2
  • pltOvrHm(): use lowercase ‘p’ instead of ‘P’ in heatmap colorbar legend

  • MPAC’s full name is changed to ‘Multi-omic Pathway Analysis of Cell’

                      Changes in version 1.1.1
  • added new functions
  • pltOvrHm(): to plot a heatmap of over-represented gene sets for clustered samples
  • ppRunPrd(): to prepare required files to run PARADIGM
  • updated existing functions
  • conMtf(): use decompose() instead of decompose.graph() for igraph 2.0
  • ppPermInp(): increased default permutations from 3 to 100
  • ppRealInp() and ppRnaInp(): added an option rna_n_sd to set standard deviation range to define RNA state
  • pltNeiStt(): fixed bugs and adjusted output figure height
  • colPermIPL() & fltByPerm(): added a threads option to parallelize
  • runPrd() & runPermPrd(): when no sampleids is provided, all the samples in input real_se and perml will be used.
  • subNtw(): entities with NA values in all samples in the input fltmat will be ignored.
  • updated tests
  • test-conMtf() & test-subNtw(): use as_edgelist() instead of get.edgelist() for igraph 2.0
  • test-conMtf() & test-ovrGMT(): add upgrade_graph() on extdata

msa

                   Changes in version 1.39.5

  • workaround to avoid segfault caused by ClustalOmega

                     Changes in version 1.39.4

  • fix of gc 8.2.8 source for Windows platform

                     Changes in version 1.39.3

  • upgraded gc library to version 8.2.8

  • changed compiler standard to gnu++11 for ClustalOmega compilation on Linux/Mac

  • fixed a bug regarding passing file names as inputs

                     Changes in version 1.39.2

  • further fix to cope with the upcoming change to C23 as default in R 4.5.0

                     Changes in version 1.39.1

  • added USE_C17 to DESCRIPTION as SystemRequirements to cope with the upcoming change to C23 as default in R 4.5.0

MSA2dist

             Changes in version 1.11.2 (2025-03-28)

  • update DRESCRIPTION

               Changes in version 1.11.1 (2024-11-14)

BUG FIXES

  • fixed pal2nal
  • fixed aastring2aabin to return alignment

NEW FEATURES

  • added globalDeletionAA

MsBackendMassbank

                    Changes in version 1.15

Changes in 1.15.3

  • Fix import from MassBank txt files:
  • force ordered m/z values
  • skip import of deprecated records
  • introduce sanity checks on spectra variables.

Changes in 1.15.2

  • Import extractByIndex() from ProtGenerics.

Changes in 1.15.1

  • Complete unit test coverage.

MsBackendMetaboLights

                     Changes in version 1.1

Changes in 1.1.4

  • Remove debug message.

Changes in 1.1.3

  • Add mtbls_delete_cache() to delete locally cached files for a specified MetaboLights ID.
  • Change unit tests to only remove selected content instead of wiping the full cache.

Changes in 1.1.2

  • Fetch and cache each data file individually.
  • Retry retrieval of data from MetaboLights up to 3 times before throwing an error message, with an increasing time period between attempts.

MsBackendMgf

                    Changes in version 1.15

Changes in 1.15.3

  • Add support for peak annotations in MGF files.

Changes in 1.15.2

  • Fix missing links in the documentation.

Changes in 1.15.1

  • Complete unit test coverage.

MsBackendMsp

                    Changes in version 1.11

Changes in 1.11.1

  • Complete unit test coverage.

MsBackendSql

                     Changes in version 1.7

Changes in 1.7.4

  • Fix handling of parameter msLevel. in filterRt().

Changes in 1.7.3

  • Add new peaks data storage mode blob2 which stores the full peaks matrix as a single entity to the database table.
  • Change default peaks data storage mode to blob2.
  • Add parameter peaksStorageMode to database creation function allowing to select the new peaks data storage mode.
  • Add mz() and intensity() methods.
  • Small performance improvements for peaksData() using fmatch() from the fastmatch package and avoiding to re-order the results if not needed.
  • Performance improvement for blob and blob2 storage modes by using xda = FALSE in serialize().
  • Complete unit test coverage.

Changes in 1.7.2

  • Import extractByIndex from ProtGenerics.
  • Add missing links in documentation.

Changes in 1.7.1

  • Complete unit tests to cover all code lines.

MsCoreUtils

                    Changes in version 1.19

MsCoreUtils 1.19.2

  • Fix reduce() to merge also ranges with the same end.

MsCoreUtils 1.19.1

  • Add new reduce() function to reduce overlapping numeric ranges to disjoint ranges.

MsDataHub

                     Changes in version 1.7

MsDataHub 1.7.4

  • Fix documentation.

MsDataHub 1.7.3

  • Add cRAP contaminant databases.

MsDataHub 1.7.2

  • Fix space in latest resource URLs.

MsDataHub 1.7.1

  • DIA-NN report files from Ai et al (2025) for adult and iPSC-derived cardiomyocytes single-cell proteomics data.

MsExperiment

                     Changes in version 1.9

MsExperiment 1.9.1

  • Small fixes and update to MsBackendSql version >= 1.7.3.

MSnbase

                    Changes in version 2.33

MSnbase 2.33.5

  • Remove methods-fragments.R (is now part of PSMatch).

MSnbase 2.33.4

  • Fix bug in MzTab() (see issue #608).

MSnbase 2.33.3

  • Fix failing unit test.

MSnbase 2.33.2

  • Fix the pheplus1 code chunk in MSnbase-demo vignette to handle the new Rdispo::getIsotope() list return value.

MSnbase 2.33.1

  • Add functionality to convert a Spectra object to a MSpectra.
  • Suggest pRolocdata (>= 1.43.2.1) (that has some extdata, needed to other packages’ vignettes).

MSnbase 2.33.0

  • New Bioc devel version

msqrob2

                   Changes in version 1.15.1

  • fix: fixed fnames in cptac vignette and moved away from msdata to rely on MsDataHub instead

                      Changes in version 1.15                         

                 Changes in version 1.15.0

  • New Bioconductor devel release 3.21

                     Changes in version 1.14.1
  • Added more flexibility in the msqrobLM function for models with missing variables
  • Fixed full rank check for models without ridge in certain cases

MSstatsTMT

             Changes in version 2.14.1 (2024-10-30)

  • Added interactive plotting functions using Plotly.

  • Integrated support for ProteinProspector data conversion via MSstatsConvert.

MultiAssayExperiment

                   Changes in version 1.34.0

New features

  • Replace longFormat generic and methods with longForm (@lgatto, #333)
  • Use h5mread::h5writeDimnames instead of HDF5Array::h5writeDimnames
  • Add note to warning message in saveHDF5MultiAssayExperiment to use loadHDF5MultiAssayExperiment to reliably load data

Bug fixes and minor improvements

  • Add package anchors to links in documentation
  • Optimize subsetByColData (@leopoldguyot, #334)
  • Use BiocBaseUtils::checkInstalled to check for Suggests packages
  • Additional checks for j and … in double bracket [[ MultiAssayExperiment method

multistateQTL

             Changes in version 1.99.5 (2025-03-17)

  • Added support for additional arguments in plotting functions to be passed to ComplexHeatmap.

               Changes in version 1.99.0 (2025-03-07)

  • Patches to make multistateQTL compatible with major change to internal representations in QTLExperiment.

               Changes in version 1.3.2 (2025-01-28)
  • Fix up a test with a rounding error
  • Remove bug in getComplete where setting verbose = TRUE would lead to an error

  • Update replaceNAs test

               Changes in version 1.3.1 (2025-01-14)
  • Fix up a test that was failing due to machine tolerance

MungeSumstats

                   Changes in version 1.15.3

Bug fix

*Updated retrieval of IEU OpenGWAS to new approach requiring login. Also updated to use the IEU OpwnGWAS R package as a dependency.

                   Changes in version 1.15.2

New features

*FAQ Website updated.

                   Changes in version 1.15.1

New features

*FAQ Website added.

mzR

                   Changes in version 2.41.4

  • Use “rtime” and “intensity” as column names for the data.frame returned by chromatogram(). Fixes #304.

                     Changes in version 2.41.3

  • Fixed off-by-one indexing issue with index access for chromatogramHeader vs chromatogram. Fixes #302. Thanks Nils Hoffmann !

                     Changes in version 2.41.2

  • Report also electron beam energy (MS:1003410) for EAD data.

                     Changes in version 2.41.1

  • Fix compilation error with stricter compiler checks

NADfinder

                   Changes in version 1.31.1
  • Update email address.

NanoMethViz

                    Changes in version 3.4.0
  • Fixed modbam_to_tabix() to not delete existing directories when provided as the output file. Previously it would delete the directory and create a file with the same name, now it will fail if the output is a directory.

NanoTube

                   Changes in version 1.13.1
  • processNanostringData now reads RCC files recursively from the parent directory, so that it can handle RCC files within subfolders.

nullranges

                   Changes in version 1.13.1
  • Removing unevaluated code in vignette

OmnipathR

                    Changes in version 4.0.0

Features

  • ID translation ambiguity analysis
  • KEGG REST API client
  • New metabolomics resources: HMDB, RaMP, Chalmers Sysbio GEMs, STITCH,
  • Metabolite-protein interactions from MetalinksDB
  • Metabolite ID translation using RaMP and HMDB data

Technical

  • Rewritten and improved parameter processing for OmniPath queries
  • Rewritten downloaders based on curl and httr2
  • Fine control over curl handlers
  • Detailed log messages about HTTP requests
  • Diagnostic log messages: session info, libraries, versions, platform info, curl options, HTTP timings, headers
  • Option to include curl debug log in the log file
  • Robust TCP keep-alive parameters that hopefully fix rest.uniprot.org dowloads

OncoSimulR

             Changes in version 4.9.1 (2025-03-04)
  • Fix three Notes in Rmd files.

ontoProc

                    Changes in version 2.1.7

  • update the module dependencies in basilisk.R

  • add quickOnto() for convenient retrieval of OIRDS serialized ontologyIndex instances in cache

OutSplice

             Changes in version 1.7.1 (2025-02-03)

  • Added warning message for only having 1 Tumor Sample

  • Updated vignette file

pairedGSEA

                    Changes in version 1.7.0
  • Ensure compatibility with updated msigdbr and new R version
  • Fixed rare bug in aggregate_pvalue

pathview

                   Changes in version 1.47.1

  • fix “R CMD check” error caused by some problem in org.EcK12.eg.db

  • remove org.EcK12.eg.db from Suggests for BioC build check

  • korg now include 10718 KEGG species or 951 new species beyond March 2024.

pcaExplorer

                    Changes in version 3.2.0

Other notes

  • Some changes in the source of the documentation, providing anchors to all function calls. This avoids the new note in R CMD check in the new major release

Pedixplorer

                    Changes in version 1.3.4
  • Add example of interactivness in vignette
  • Fix label adjusting position in plot functions

  • Fix arrow size in ggplot

                      Changes in version 1.3.1
  • Add support for .ped, .tsv files in data import
  • is_informative independent from useful_inds
  • Use directly columns names from fill instead of the mods columns
  • Move to R 4.4 and Bioc 3.20
  • Fix unittests and update snapshots
  • Change normalisation process to directly use id, dadid, momid, famid, sex no more need for indId, fatherId, …
  • affection is now used as default affection modality columns that will be used to generate affected
  • status is replaced by deceased
  • steril is replaced by fertility and corresponding symbols is added for infertile and infertile_choice_na
  • terminated sex code is replace by miscarriage new slot
  • miscarriage, evaluated, consultand, proband, carrier, asymptomatic and adopted are now recognize and use for plotting
  • Argument order of Ped() as changed when using vectors. This choice has been made for a better consistency across the package. Please check that your argument are properly named (i.e. sex has been moved after famid and avail after deceased).
  • Shiny application is updated and improved (aesthetics, errors, warnings, functionnalities).
  • Add dateofbirth and dateofdeath to the Ped object
  • Changee from round to signif for the precision argument
  • Improve stability of test by adding and controlling the options() and par() arguments in the unittests.
  • Carrier symbols is proportional to the mean of the box size

pgxRpi

             Changes in version 1.3.3 (2025-02-12)
  • Updated the “sample_count” extraction method from “services/collations” to beacon count response, expanding counts to include all available entities (analyses, biosamples, individuals) and changing the type from “sample_count” to “counts” in pgxLoader.
  • Enabled parallel queries across multiple resource domains (in pgxmetaLoader).

  • Optimized code for Beacon response mapping and updated YAML mapping rules.

  • Updated pgxfreqplot to set ylim as max(lowfreq, highfreq), ensuring proper scaling when high-level frequency exceeds low-level frequency.
  • Replaced id parameter with the standard query path for Beacon queries.

  • Modified variant data retrieval in seg format to fetch directly from the service API.

               Changes in version 1.3.1 (2025-01-14)
  • Removed the pgxFilter function and incorporated its functionality into pgxLoader with the “filtering_terms” type, following the Beacon v2 response mapping.
  • Updated vignette filenames for improved clarity.
  • Made parameter checks more flexible for Beacon queries.

PhyloProfile

                    Changes in version 2.0.0

  • runtime significantly improved #105

                     Changes in version 1.20.4

  • added t-SNE dimension reduction

  • highlight genes and taxa for sub-plot

  • use fastcluster for clustering and sorting the input taxa

                     Changes in version 1.20.3

  • fixed bug with NCBI taxonomy link at the first time running

  • improve UMAP 3D (hover info, dot zooming, same colors with 2D plot)

                     Changes in version 1.20.2

  • hover option for UMAP

  • UMAP 3D using plotly

  • fixed bug with Point’s info

                     Changes in version 1.20.1

  • auto identify refspec

  • fixed subsetting data using a list of gene IDs

PoDCall

             Changes in version 1.15.1 (2024-12-19)
  • Modified results table

POMA

                   Changes in version 1.17.6
  • Allow grouping variable selection in PomaImpute
  • New documentation

pRoloc

                    Changes in version 1.47

Changes in version 1.47.5

  • Remove long title in mcmc_plot_probs

Changes in version 1.47.4

  • Addition of UMAP as a dimensionality reduction method in plot2D
  • In this version there have been several new arguments to the plot2D function to improve visualisation. Please see below.
  • A new argument bg has been added to plot2D to allow the use of filled point characters see issue #153
  • plot2D also has a new argument called palette to facilitate the generation of nice colour schemes to work with filled point characters
  • The functions setStockbg, getStockbg, setUnknownbg and getUnknownbg have been added for colour management
  • The behaviour of the function addLegend when called with argument where = “other”. The call to dev.new() has been removed so that instead of opening a new device and plotting the legend it instead plots the legend on an empty plot in the current window.
  • The default of grid in plot2D has been changed to FALSE.
  • All plotting arguments now have an argument unknown for the specification of how unlabelled points are defined. Default is still “unknown”.

Changes in version 1.47.3

  • Deprecate setAnnotationParam, getAnnotationParams, showGOEvidenceCodes, getGOEvidenceCodes, addGoAnnotations, orderGoAnnotations and associated helper functions
  • Remove vignette v04 for adding GO annotations
  • Update getting started vignette v01 with clustDist (previously in v04)
  • Update the transfer learning vignettes to reflect the deprecation of GO functions

Changes in version 1.47.2

  • Bump version to propage to landing page

Changes in version 1.47.1

  • Lisa Breckels is now maintainer.

Changes in version 1.47.0

  • New devel version

ProtGenerics

                   Changes in version 1.39.2

  • Move applyProcessing(), processingChunksize(), processingChunkSize()<- and processingChunkFactor() generics from the Spectra package.

                     Changes in version 1.39.1

  • Add extractByIndex() generic.

PSMatch

                    Changes in version 1.11

PSMatch 1.11.5

  • Correct plotSpectraPTM annotations.

PSMatch 1.11.4

  • Added plotSpectraPTM: a plotting function to visualise post-translational modifications.

PSMatch 1.11.3

  • Deprecated addFragments. The use of labelFragments is endorsed instead. See PR #20.

PSMatch 1.11.2

  • Replace calculateFragments with calculateFragments2. See PR #19.

PSMatch 1.11.1

  • New calculateFragments2 function includes fixed and variable modifications to fragments ions. See PR #16.

PSMatch 1.11.0

  • New devel version

PureCN

                   Changes in version 2.14.0

SIGNIFICANT USER-VISIBLE CHANGES

  • Do not filter allosome coverage for male samples.

BUGFIXES

  • Fixed large runtime of readAllelicCounts. Thanks luyh-xp (#378).

  • –bai was ignored in Coverage.R except for lists (#272). Thanks @nspies-carisls and @lbeltrame.

pwalign

                    Changes in version 1.4.0
  • No significant changes in this version.

QFeatures

                    Changes in version 1.17

QFeatures 1.17.5

  • Remove superfluous message when filtering with keep = TRUE (see issue 231).

QFeatures 1.17.4

  • Optimisation of aggregateFeatures in the case of multiple assays aggregation.

QFeatures 1.17.3

  • Fix bug in nNA() on empty assays (see #174).

QFeatures 1.17.2

  • Fix fnames argument in readQFeatures(). The fnames argument is not passed to readSummarizedExperiment() anymore, but used at in readQFeatures(). Rownames are now set after splitting. Given that rownames must be unique and that this was enforced with make.unique(), the previous behaviour misnamed features that should get the same name.

QFeatures 1.17.1

  • Fix: solved readQFeatures() bug and adapted unit tests.
  • Docs: created new vignette about reading data with QFeatures

QFeatures 1.17.0

  • New Bioconductor 3.21 (devel) release

QTLExperiment

             Changes in version 1.99.1 (2024-03-05)

  • Major update to the underlying representation of the slots. o Slots now use elementMetadata and colData. o No longer use internal col and row Data. o Almost all functions have been updated and testing is working but there may still be some edge cases that I have missed. o Better consistency with other child classes of SingleCellExperiment.

               Changes in version 1.5.0 (2024-10-30)

  • Added a test for object validity error messages

RaggedExperiment

                   Changes in version 1.32.0

Bug fixes and minor improvements

  • Added package anchors to links in documentation

RAIDS

                    Changes in version 1.5.1

SIGNIFICANT USER-VISIBLE CHANGES

o Intagration of Rsamtools

ramr

             Changes in version 1.15.2 (2025-03-06)

  • complete rewrite of getAMR and simulateData for speed and robustness

               Changes in version 1.15.1 (2024-12-17)

  • zero-and-one inflated beta distribution by gamlss.dist::BEINF

  • cleaner plots

Rarr

                     Changes in version 1.7
  • Added path() method for ZarrArray class that returns the location of the zarr array root.
  • Removed used of non-API call SETLENGTH in C code.
  • Small changes to compilation of internal blosc libraries to cope with the C23 compiler becoming the default in R-4.5.0

rawDiag

                     Changes in version 1.3
  • adapt to rawrr changes

rawrr

                    Changes in version 1.15

  • Add Leo as author.

  • Replace mono with dotnet; Introduced a statically linked runtime rawrr assembly for Windows, Linux, and macOS on x64 architectures, streamlining installation and usage #75.

  • Consistently normalize paths #76.

RCy3

                   Changes in version 2.28.0
  • No changes since version 2.26.0.

ReactomeGSA

             Changes in version 1.21.1 (2024-11-07)
  • Added new functions to perform quantitative comparative pathway analyses for scRNA-seq data.

RegionalST

                    Changes in version 1.5.6
  • Fix bugs when plotting figures with BayesSpace

RESOLVE

                   Changes in version 1.10.0

  • Major code update, implementing signatures-based clustering and associations to signatures exposures.

  • Package released in Bioconductor 3.21.

rGREAT

                    Changes in version 2.9.1

  • change NCBI api to v2.

  • use exp(phyper(..., log.p = TRUE)) to get rid of zero p-values. Thank @andvon for the code contribution.

rhdf5

                   Changes in version 2.52.0

CHANGES

  • Removed used of the non-API STRING_PTR function when permuting string datasets.

Bug fixes

  • Fixed overflow when trying to write a large number of very long strings. Backported to 2.50.1. (Thanks to Aaron Lun @LTLA for reporting this https://github.com/grimbough/rhdf5/issues/151).

  • Addressed potential issued caused by undefined compiler behaviour when arrays of length zero were being created in C code. Backported to 2.50.2 (Thanks to Prof B. Ripley for reporing this.)

rhdf5filters

                   Changes in version 1.20.0
  • Small changes to compilation of internal blosc and vbz libraries to cope with the C23 compiler becoming the default in R-4.5.0

BUG FIXES

  • Ensure PKG_CPPFLAGS are passed to all compilation step. This was an issue in the case where R was installed via conda and package binaries were not available. Backported to version 1.18.1.

Rhtslib

                    Changes in version 3.4.0
  • No significant changes in this version.

RiboDiPA

                   Changes in version 1.15.1
  • Rcpp function centerCPP.cpp was modified so it can take reads aligned to more than 10 consecutive regions in the genome. Ribo-seq read should typically align to no more than three consecutive blocks in the genome.

ribosomeProfilingQC

                   Changes in version 1.19.2

  • Export the reads distribution with considering the precedence.

                     Changes in version 1.19.1

  • Update email address.

ROTS

                    Changes in version 2.0.0
  • Added support for linear and mixed-effects models

rpx

                    Changes in version 2.15

rpx 2.15.1

  • Fix error due to remote side change (another one).

rpx 2.15.0

  • New devel version (Bioc 3.21)

Rsubread

                   Changes in version 2.22.0
  • Improved identification and reporting of junction counting functionality in featureCounts.

rWikiPathways

                   Changes in version 1.28.0
  • None

S4Arrays

                    Changes in version 1.8.0

NEW FEATURES

  • arep_times() and arep_each(): multidimensional versions of base::rep( , times=) and base::rep( , each=).

  • as_tile(): a convenient way to control the direction of recycling in the context of arithmetic and other binary operations between an array and a vector, or between two arrays of distinct dimensions. Still work-in-progress!

  • kronecker() methods for Array objects that work out-of-the-box on Array derivatives that support [ and *.

S4Vectors

                   Changes in version 0.46.0

NEW FEATURES

  • Add ‘margin’ argument to wmsg() internal helper.

SIGNIFICANT USER-VISIBLE CHANGES

  • Expose ranges_mapper() and positions_mapper() thru the S4Vectors C interface.

SCArray

                   Changes in version 1.16.0
  • update according to the SparseArray package

SCArray.sat

                    Changes in version 1.8.0
  • update according to DelayedArray & SparseArray

scater

                   Changes in version 1.36.0
  • Add min.value,max.value arguments to plotReducedDim to enable truncating colour scales using a numeric value or a quantile (eg “q10”).

scDotPlot

                    Changes in version 1.1.1
  • Enabled clustering for a group with annotations for a single feature

scoup

                    Changes in version 1.1.1

  • Improved flexibility by allowing specification of mutation rate parameters.

  • Adjusted the fixed input in codonCoeffs function.

  • Reversed the mutation matrix flexibility due to expensive computational cost.

  • Updated help files to aptly emphasise episodic in-place of “deterministic”.

  • Revised the codonFreq function so that it uses softmax identity.

scp

                    Changes in version 1.17

scp 1.17.1

  • Deprecate aggregateFeaturesOverAssays, use QFeatures::aggregateFeatures instead.

scp 1.17.0

  • New Bioconductor 3.21 devel

scrapper

                     Changes in version 1.2

  • Added the aggregateAcrossGenes() function, to compute an aggregate expression value for gene sets.

  • Added compute.cohens.d=, compute.delta.mean= and compute.delta.detected= options to scoreMarkers().

  • Support top=Inf in chooseHighlyVariableGenes(). Also added the bound= argument to set a hard upper/lower bound.

  • Bugfix for correct filtering with block= in the various filter*QcMetrics() functions when not all blocking levels are present.

  • Bugfix to clusterKmeans() to respect the user-supplied seed= in relevant initialization methods.

  • Added a return.graph= option to return the SNN graph from runAllNeighborSteps().

  • Added a testEnrichment() function for quick and dirty gene set enrichment testing.

  • Modified runPca() so that it caps number= to the maximum number of available PCs.

  • Added an analyze() function that provides a one-click approach for analyzing single-cell data.

  • Added a reportGroupMarkerStatistics() function to combine all marker statistics for a single group into one data frame.

  • Switch clusterGraph() to use C++ wrappers around the igraph community detection algorithms via Rigraphlib. This replaces the dependency on the igraph R package.

  • Added a delayed= option to avoid wrapping the matrix in a DelayedArray in normalizeCounts().

scRepertoire

                    Changes in version 2.3.2

UNDERLYING CHANGES

  • Fixed issue with denominator in getCirclize()

  • Fixing chain issue with clonalCompare() - expanded assertthat statement

                      Changes in version 2.2.1
  • Rebasing for the purposes of Bioconductor version 2.2.0

NEW FEATURES

  • Added support for BCRs for loading ParseBio sequences.
  • Added quietBCRgenes() and quietTCRgenes() from Ibex and Trex and quietVDJgenes() as a convenience that runs both. The functions filter out known TCR and/or BCR gene signatures.

UNDERLYING CHANGES

  • Added Seurat to the Suggests field in the DESCRIPTION file.

scRNAseqApp

                   Changes in version 1.7.14

  • Add function extractFragmentNameMapList.

                     Changes in version 1.7.13

  • Add search for token.

                     Changes in version 1.7.12

  • Fix the token issue.

                     Changes in version 1.7.11

  • Fix the issue if the data list is not updated for the main page.

                     Changes in version 1.7.10

  • Fix multiple typos.

                      Changes in version 1.7.9

  • Update the footnote.

                      Changes in version 1.7.8

  • Remove the import of X11Fonts.

                      Changes in version 1.7.7

  • Update email address.

                      Changes in version 1.7.6

  • Add fragmentNameMap to createDataset.

  • Add fragmentNameMap to createDataset.

                      Changes in version 1.7.5

  • Optimize read and save ATAC peak matrix.

                      Changes in version 1.7.4

  • Add module ExplorerAcc.

                      Changes in version 1.7.3

  • check parameters before creating dataset.

                      Changes in version 1.7.2

  • add binSize parameter for atac bigwig files.

                      Changes in version 1.7.1

  • fix the bug if no signals for atac coverage and invalid filenames.

SeqArray

                   Changes in version 1.48.0

NEW FEATURES

  • seqAddValue(): use bit1 for a logical vector; new argument ‘use_float32’ for storing double

  • new argument ‘start’ in seqResetVariantID()

  • new argument ‘digest’ in seqRecompress() to add MD5 hash codes

  • seqGetData(, "$chromosome") returns chromosome codes in an object of ‘S4Vectors::Rle’

  • seqGetData(, .tolist=NA) returns an extended list defined in IRanges (e.g., IntegerList) when it is applicable

  • seqListVarData(, useList=TRUE) returns an extended list defined in IRanges

UTILITIES

  • Tweak display in seqResetVariantID()

  • use crayon::silver() instead of crayon::blurred() in the display since RStudio blurs the screen output

BUG FIXES

  • seqBlockApply() should recover the filter when the user-specified function fails

                     Changes in version 1.46.2

UTILITIES

  • seqVCF_Header() allows multiple cores to calculate the total number of variants when ‘getnum=TRUE’ (the Rsamtools package should be installed); seqVCF2GDS() is faster when obtaining the number of variants for splitting files.

  • new ‘variant_count’ in seqVCF2GDS() to specify the number of variants in the VCF file when it is known or an approximation is known; it is only applicable when multiple cores are used. If ‘variant_count’ is specified, counting the number of variants will be skipped.

SingleCellAlleleExperiment

                    Changes in version 1.3.2

Fixing error in vignette regarding the knee plot in 3.21 devel / R4.5 Removing the fitted line from knee plot

                    Changes in version 1.3.1

Fixing error in vignette regarding the knee plot in 3.21 devel

                    Changes in version 1.3.0

No changes, devel version bump due to new bioconductor 3.21 devel branch

SingleCellExperiment

                   Changes in version 1.30.0
  • Preserve NAs in the input matrices to rowPairs() and colPairs() converting them to SelfHits.

singleCellTK

             Changes in version 2.16.1 (2024-02-12)
  • Fixed decontX/soupX webapp error
  • Fixed error in reportCellQC
  • Fixed additional bugs with Seurat V5 integration

SingleR

                   Changes in version 2.10.0

  • Switch to scrapper for DE detection when de.method=”t” or de.method=”wilcox” in trainSingleR(). This should give similar results to but is faster than the previous scran functions.

  • Switch to scrapper for variance calculation, PCA and clustering in aggregateReference(). This should be faster than the previous BiocSingular and stats::kmeans functions, and avoids the need to consider the seed.

  • Added a configureMarkerHeatmap() function to perform all the calculations used by plotMarkerHeatmap(). This allows users to re-use the calculations with a custom visualization for the expression values.

  • Automatically remove duplicated gene names in trainSingleR(). This avoids matching to the wrong gene after identifying markers from the reference dataset.

  • Report scores as a DataFrame of nested Dataframes in combineRecomputedResults(). Each inner DataFrame corresponds to a reference and contains the identity of the best label and the recomputed score in that reference. This is simpler and more efficient than the previous “expanded with NA” format.

  • Report the deltas (i.e., difference between the best and next-best scores) in combineRecomputedResults().

  • Separate the missingness check arguments in SingleR() with the new check.missing.test= and check.missing.ref= options. The former is disabled by default, to avoid an unnecessary missingness check in the vast majority of test cases.

  • Added a fine.tune.combined= option to classifySingleR(), to disable fine-tuning only when combining multiple references. This allows users to recover pre-2.8.0 behavior and trades accuracy for speed.

  • Removed the deprecated combineCommonResults() function.

smartid

                    Changes in version 1.3.2

  • Update batch param in top_markers function.

                      Changes in version 1.3.1

  • Update top_markers function to allow batch correction for glm method.

sparrow

                    Changes in version 1.14

Enhancements

  • Updated to support refactored msigdbr package (version >= 10.0.0), which now only includse the human Hallmark genesets internally. The msigdbr package relies on an external (non CRAN) msigdbdf package, for the rest of the (now more recent) definitions of the MSigDB gene set collections.

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.

SparseArray

                    Changes in version 1.8.0

NEW FEATURES

  • Make rowsum() and colsum() work on any dsparseMatrix derivative and not just on a dgCMatrix object. For example now they also accept a dgRMatrix or dgTMatrix object.

  • Make crossprod(), tcrossprod(), and %*% work between a SparseMatrix object and an ordinary vector.

  • Arith operations between a SparseArray (or NaArray) object ‘x’ and an atomic vector ‘y’ are no longer restricted to the latter being a single value: now the length of the latter can also be ‘dim(x)[[1]]’ or a divisor of it.

BUG FIXES

  • Make sure that SparseArray(x) and SVT_SparseArray(x) always propagate the dimnames.

  • Fix bug in Math and Math2 operations on SVT_SparseArray and NaArray objects.

spatialHeatmap

             Changes in version 2.13.1 (2024-11-23)
  • Added project wibsite in vignettes.

Spectra

                    Changes in version 1.17

Change in 1.17.10

  • Accept labels argument as a list instead of a character in the plotting functions.

Change in 1.17.9

  • Allow parameter msLevel. = integer() for filterRt() to filter spectra of all MS levels. This was msLevel. = uniqueMsLevels(), which, depending on the backend, can be computationally intense. Add related unit tests to the unit test suite.

Change in 1.17.8

  • Add parameter return.type to peaksData().

Change in 1.17.7

  • Add the spectraVariableMapping<- generic method.

Change in 1.17.6

  • Add new fillCoreSpectraVariables() function that allows to add eventually missing core spectra variables (with the correct data type) to a data frame.

Change in 1.17.5

  • Move generics processingChunkSize(), processingChunkFactor() and applyproceesing() to ProtGenerics. Required ProtGenerics version 1.39.2 or higher. These were moved to be able to implement them in the Chromatograms package.

Change in 1.17.4

  • Import extractByIndex() from ProtGenerics.

Change in 1.17.3

  • Fix cbind2() unit test for backends that fails if the number of spectra in the tested backend is (by chance) equal to 4.

Change in 1.17.2

  • Add cbind2() method to easily add multiple spectraVariables and their content to the spectraData of a Spectra object. See also issue #342

Changes in 1.17.1

  • Refactor containsMz() to support chunk-wise processing.

SPIAT

                    Changes in version 1.9.0

Development version on Bioconductor 3.21.

SpotSweeper

                    Changes in version 1.3.2

Minor Changes

  • Broadened Compatibility: Updated all functions to use inherits(spe, “SpatialExperiment”) instead of checking class(spe) directly. This change ensures that derived classes (e.g., SpatialFeatureExperiment) are also supported, improving flexibility and ease of use.

New Features

  • Added the ‘flagVisiumOutliers()’ function to identify and flag systematic outlier spots in Visium datasets. This feature enhances data quality by allowing users to efficiently detect and exclude problematic spots from downstream analyses.

                      Changes in version 1.3.1

Major Changes

  • Function Renaming: The function plotQC has been renamed to plotQCmetrics to better reflect its purpose. The new function plotQCmetrics should be used moving forward. This change improves clarity in the package’s API by specifying that this function is designed for plotting QC metrics.

New Features and Enhancements

  • shape argument: Added a shape argument to findArtifacts, allowing users to specify the neighborhood shape as either “hexagonal” or “square” for local variance calculations. This enhancement provides flexibility for different spatial arrangements in spatial transcriptomics data.

  • Updated n_order parameter: Renamed the n_rings parameter to n_order in the findArtifacts function to better describe its purpose of specifying the N-order neighbors for local mitochondrial variance calculations.

  • Parallelization: Added a workers argument for parallel processing using BiocParallel in both localOutlier and localVariance functions. This allows for faster computation, particularly on larger datasets.

Deprecations

  • plotQC Function Deprecated: The plotQC function is now deprecated. While it remains available for backward compatibility, users are encouraged to transition to plotQCmetrics. Calling plotQC will display a warning, reminding users of the deprecation.

This change is backward compatible; existing code using plotQC will still work but will show a warning. We recommend updating your code to use plotQCmetrics to avoid any issues in future versions where plotQC may be removed.

sRACIPE

                   Changes in version 1.99.0

  • New interaction types added

  • Convergence testing for deterministic simulations added

  • Ornstein-Uhlenbeck noise option added

statTarget

                     Changes in version 2.0

NEW FEATURES

  • New GUI o Mouse Hover for help information o .log file

  • New Signal correction o Combat for QC-free Signal correction o QC-RFSC methods for metabolomics and proteomics data

  • New feature slection o Random Forest and the Permutation based variable importance measures o new MDSplot for Random Forest o P-value based importance plot

  • New data preprocessing o PQN/SUM/none normalization o center/none Scaling method

structToolbox

                   Changes in version 1.19.2

  • fix pca_biplot

                     Changes in version 1.19.1

  • fix ANOVA output with interaction terms

SummarizedExperiment

                   Changes in version 1.38.0
  • No changes in this version.

SynExtend

                   Changes in version 1.19.11
  • Fixes bug where ExoLabel wouldn’t handle multiple files correctly
  • ExoLabel now reads in networks roughly twice as fast
  • ExoLabel now correctly skips negative weighted edges
  • Various improvements to ExoLabel output formatting

  • Enables experimental tuning of distance scaling in ExoLabel attenuation

                     Changes in version 1.19.10
  • Fixes critical bug in ExoLabel that previously caused large networks to always report a single large cluster

  • ExoLabel no longer allows negative weights to become positive via attenuation (positive weights can still become negative)

                     Changes in version 1.19.9
  • Bugfixes to ExoLabel
  • ExoLabel now defaults to use_fast_sort=TRUE
  • Various QoL changes for ExoLabel(…, return_table=TRUE)

  • ExoLabel now correctly reports timing

                     Changes in version 1.19.8
  • ExoLabel has a new parameter to tune the performance of hop-length attenuation.

  • Documentation and formatting updates.

                     Changes in version 1.19.7
  • ExoLabel now uses hop-length attenuation to mitigate formation of massive communities.
  • ExoLabel no longer supports inflation, since attentuation does a better job handling this without introducing additional parameters.

  • ExoLabel will now print a lot less when running with verbose=TRUE in non-interactive mode – just as informative, but less junk caused by lots of unrendered carriage returns.

                     Changes in version 1.19.6

  • fixes multiple bugs in EstimRearrScen

                     Changes in version 1.19.5

  • fixes bug in GeneVector.EvoWeaver that could affect DNA-based analyses

                     Changes in version 1.19.4
  • fixes bug that prevented building on Windows

  • adds multiple clustering support for ExoLabel

                     Changes in version 1.19.3
  • ExoLabel will no longer crash when given a network lacking a trailing newline

  • Various internal improvements and code refinements

                     Changes in version 1.19.2
  • Lots of bug fixes for ExoLabel

  • ExoLabel now reports disk consumption during execution

                     Changes in version 1.19.1
  • ExoLabel is even faster due to in-place external sort for faster file I/O

  • Other quality of life improvements to ExoLabel

                     Changes in version 1.19.0
  • First development version of Bioconductor 3.21

systemPipeShiny

                   Changes in version 1.18.0

Major Change

  • Update to systemPipeR 2.12 and systemPipeRdata 2.10
  • Add support for Single Cell RNAseq, BLAST, and Cheminformatics workflows which are new in systemPipeR.

Minor Change

  • use esquisse_container instead of esquisseContainer due to the new version of {esquisse}.

Bug Fix

  • Fix shiny 1.10 update that caused some buttons not working.
  • Fix welcome page logo animation not working, now remove the animation.
  • Fix checkModulePkgs_internal had wrong logic when all packages are installed. Now return the correct value.

tadar

                    Changes in version 1.6.0
  • Deprecated dar_val arg of assignFeatureDar()

TargetSearch

                   Changes in version 2.10.0

SIGNIFICANT USER-VISIBLE CHANGES

  • The method libId is deprecated. Use the fully equivalent function makeIndex. This method was mostly used internally, so it should not cause disruption.

NEW FEATURES

  • New method libUID which sets or gets the metabolite library unique identifiers. Previously, there was no method to change them after import.

BUG FIXES

  • Use SET_INTEGER_ELT to set an integer in the C code. The wrong macro was used for unknown reasons. This generated an error on newer R.

INTERNAL

  • Replace the memory allocation functions due to STRICT_R_HEADERS being enabled (Calloc, Free => R_Calloc, R_Free)

TBSignatureProfiler

                   Changes in version 1.19.0

Minor Changes

  • Updated gene name update mechanism in runTBsigProfiler to sum genes with identical names

Bug Fixes

  • Fixed issue with GSVA needing a non-data.frame object in runTBsigProfiler

TENxIO

                   Changes in version 1.10.0

Bug fixes and minor improvements

  • Removed projection from the show method
  • Fixed a missing anchor in @inheritParams documentation
  • The TENxH5 constructor properly validates remote files with .validateRanges
  • imported slotNames from the methods package

tomoseqr

             Changes in version 1.11.1 (2022-10-25)
  • Made the following changes: o Added 3D visualize function to imageViewer o Changed normCount and normMask options in estimate3dExpressions() to normalize option. When it is TRUE (default), the function works as if normCount = "count", normMask = TRUE. When it is FALSE, the function works as if normCount = "none", normMask = FALSE.

topconfects

                   Changes in version 1.23.2

  • Signed color palette in plot_confects_me2().

                     Changes in version 1.23.1

  • Add plot_confects_me2().

topdownr

                   Changes in version 1.29.1
  • Adapt .calculateFragments to changes in PSMatch::calculateFragments introduced in PSMatch:PR19.

  • Replace partial matching arguments with complete argument names.

                      Changes in version 1.29

trackViewer

                   Changes in version 1.43.7

  • Fix a potential bug in reading sparse cool file.

                     Changes in version 1.43.6

  • Update email address.

                     Changes in version 1.43.5

  • Add line and histogram to tracktype for trackstlye.

                     Changes in version 1.43.4

  • Remove the clip for annotation track.

                     Changes in version 1.43.3

  • Add documentation to remove y label.

                     Changes in version 1.43.2

  • Make it possible to plot annotation for peak regions.

                     Changes in version 1.43.1

  • Make it possible to plot link for back2back interaction data.

transmogR

                    Changes in version 1.3.8

  • Added shiftByVar() to produce shifted co-ordinates which match those after incorporation of variants

                      Changes in version 1.3.1

  • Changed default behaviour of digestSalmon() to exclude ‘TPM’ and ‘effectiveLength’ assays, which are now optional via the ‘extra_assays’ argument

tximeta

                   Changes in version 1.25.1
  • Added skipRanges to summarizeToGene which allows summarization of assay data when skipMeta was used and therefore ranges should not be used / output in summarization.

UCSC.utils

                    Changes in version 1.4.0
  • No significant changes in this version.

UniProt.ws

                   Changes in version 2.48.0

SIGNIFICANT USER-VISIBLE CHANGES

  • Switched to using the httr2 package for making HTTP requests

  • Reorganized and renamed documentation for the UniProt.ws class and its methods

  • Converted unit testing framework from testthat to tinytest

  • Added the README.md file from the vignette

  • Improved handling of API responses: empty results with code 200 are now caught and handled properly

  • The collapse argument in queryUniProt now shows both OR and AND options

BUG FIXES AND MINOR IMPROVEMENTS

  • Added an example to queryUniProt()

  • Fixed formatting issues in unit tests and corrected indentation in code

  • Adjusted internal logic to support queries returning larger result sets

  • Re-added Sys.sleep() call to respect rate limits

  • Set n argument in internal use of head()

universalmotif

                   Changes in version 1.24.2

BUG FIXES

  • Incorrect version number in last NEWS update.

                     Changes in version 1.24.1

BUG FIXES

  • Fixed another missed Rcpp bounds check warning.

updateObject

                   Changes in version 1.12.0
  • No changes in this version.

ViSEAGO

                    Changes in version 1.21

  • GOterms_heatmap static image update

  • GOclusters_heatmap static image update

  • show_heatmap static image update

VisiumIO

                    Changes in version 1.4.0

New features

  • Added support for CytAssist images (@ZheFrench, #8)
  • Enabled use of alternative readers via VisiumIO.csvreader option
  • Included metadata in SpatialExperiment outputs

Bug fixes

  • Resolved issue where *_feature_bc_matrix folder checks were incorrectly triggered for non-mtx formats (@estellad, #4)
  • Fixed missing package anchor in @param documentation entries

xcms

                     Changes in version 4.5

Changes in version 4.5.4

  • Replace usage of deprecated (and removed) class NAnnotatedDataFrame with AnnotatedDataFrame.
  • Fix a bug in manualChromPeaks() that caused an error when only a single chrom peak was added.

Changes in version 4.5.3

  • Address issue #765: peak detection on chromatographic data: report a chromatogram’s “mz”, “mzmin” and “mzmax” as the mean m/z and lower and upper m/z in the chromPeaks() matrix.
  • Fix calculation of the correlation coefficient for peak shape similarity with an idealized bell shape (beta) during gap filling for centWave-based chromatographic peak detection with parameter verboseBetaColumns = TRUE.
  • Add chromPeakSummary generic (issue #705).
  • Add chromPeakSummary() method to calculate the beta quality metrics.
  • Add c() method to combine multiple XcmsExperiment objects into one.
  • Add a method to coerce from XCMSnExp to XcmsExperiment objects.

Changes in version 4.5.2

  • Small update to featureSpectra() and chromPeakSpectra() to allow addition of chromPeaks() and featuresDefinitions() columns to be added to the Spectra output.
  • Tidied the xcms vignette, to order the filtering of features and remove the outdated normalisation paragraph.In depth discussion on this subject can be found on metabonaut.

Changes in version 4.5.1

  • Fix compile errors with R-4.5

Xeva

                   Changes in version 1.23.1
  • The datasets previously available have been deprecated. downloadXevaSet will no longer work.

zellkonverter

                   Changes in version 1.18.0

New features

  • Add minimal support for SpatialExperiment objects to writeH5AD() and SCE2AnnData(). This stores the spatial coordinates in a obsm item named “spatial” as expected by the squidpy Python package. (PR from @mcmero)

Major changes

  • Add environment for anndata v0.11.4. This is now the default environment for the Python reader/writer.

  • Modify SCE2AnnData() to covert sparse matrices to dgRMatrix when they are. This mostly applies to assays and should be more compatible with what is expected by Python packages.

Minor changes

  • Add a testload argument to basiliskRun() calls which may help with problems creating Python environments

  • Updates to documentation and tests

Bug fixes

  • Improve handling of missing row or column names in SCE2AnnData()

zenith

                    Changes in version 1.8.1
  • March 19, 2025
  • fix get_MSigDB() to handle change to msigdbr
  • now use msigdbdf

NEWS from existing Data Experiment Packages

MetaScope

                    Changes in version 3.21

Major changes

  • All MetaBLAST functionality and references removed.

pRolocdata

                   Changes in version 1.45.1
  • Lisa Breckels is now maintainer.

scRNAseq

                   Changes in version 2.22.0
  • Added the listPaths() function to list available paths to subdatasets. This is now referenced by an error message in fetchDataset() when a path= is required but not supplied.

spatialLIBD

                   Changes in version 1.19.12

NEW FEATURES

  • @lahuuki added guide_point_size as a argument to vis_clus() and vis_grid_clus(), which allows controlling the size of the points in the legends for the discrete variable plots. See https://github.com/LieberInstitute/spatialLIBD/pull/104 for more details.

                     Changes in version 1.19.11

BUG FIXES

  • @Nick-Eagles fixed a bug for specifying colors in vis_clus() and related functions when NA values are present in the cluster variable. For more details check https://github.com/LieberInstitute/spatialLIBD/pull/102.

                     Changes in version 1.19.10

NEW FEATURES

  • @lahuuki added the gene_name argument to sig_genes_extract() and sig_genes_extract_all() to make these functions more flexible. See https://github.com/LieberInstitute/spatialLIBD/pull/101 for details.

                     Changes in version 1.19.9

BUG FIXES

  • @lahuuki resolved the bug we discovered on a dataset being analyzed by @Nick-Eagles as we documented at https://github.com/LieberInstitute/spatialLIBD/issues/98. Basically, an internal function used by layer_stat_cor_plot() was having issues with cluster names that were just numbers such as “1”, “2”, …, “13” where annotate_registered_clusters() could result in a “9/13” annotation but then that would match with “1”, “3”, “9”, and “13” instead of just “9” and “13”, thus introducing incorrect “X” annotations on layer_stat_cor_plot(). @lahuuki resolved this at https://github.com/LieberInstitute/spatialLIBD/pull/99.

                     Changes in version 1.19.8

NEW FEATURES

  • vis_gene() now has the cap_percentile argument as implemented by @Nick-Eagles. This allows you to cap the expression values at a certain percentiles, which can be useful to exclude super high outlier values which are common with Visium HD data. See https://github.com/LieberInstitute/spatialLIBD/pull/97 for details.

BUG FIXES

  • Fixed colors on layer_stat_cor_plot() thanks to @lahuuki. Details at https://github.com/LieberInstitute/spatialLIBD/pull/94.

                     Changes in version 1.19.7

BUG FIXES

  • Removed code that made the app very slow to load using HDF5Array objects. See https://github.com/LieberInstitute/spatialLIBD/commit/b80d92c3271a6ad92859f79a3bc343f77bad9bf2 for details.

  • Fixed a bug on the Z-score calculation in multi_gene_z_score(). See https://github.com/LieberInstitute/spatialLIBD/commit/2d17ea2c3d1b73b38fbd50503765052c8487b9b1 for details. Implemented by @Nick-Eagles.

  • Fix a bug in the documentation of run_app() for the example stitched data.

  • No longer point to Twitter, instead point to Bluesky. This is for the package main README file as well as the default app documentation files.

                     Changes in version 1.19.5

BUG FIXES

  • Fixed internal errors in add_qc_metrics() on the scuttle::isOutlier() function calls.

                     Changes in version 1.19.4

NEW FEATURES

  • @lahuuki fully re-implemented gene_set_enrichment_plot() using ComplexHeatmap::Heatmap(). This new version has several new arguments that allow adding more annotation to the resulting heatmap. See https://github.com/LieberInstitute/spatialLIBD/pull/93 for more details. This also means that layer_matrix_plot() has been removed from the package since it previously served as a helper function for gene_set_enrichment_plot().

                     Changes in version 1.19.3

BUG FIXES

  • Resolved https://github.com/LieberInstitute/spatialLIBD/issues/90 which made add_key() too strict and would create issues with export_cluster(). Reported by @lahuuki and @manishabarse.

                     Changes in version 1.19.2

BUG FIXES

  • Merged https://github.com/LieberInstitute/spatialLIBD/pull/92 by @lahuuki. This fixes https://github.com/LieberInstitute/spatialLIBD/issues/72 and https://github.com/LieberInstitute/spatialLIBD/issues/48 by making registration_pseudobulk() more robust. The original issues were reported by @boyiguo1 and @berniejmulvey.

                     Changes in version 1.19.1

NEW FEATURES

  • Merged https://github.com/LieberInstitute/spatialLIBD/pull/91 by @lahuuki. This pull request fully re-implemented layer_stat_cor_plot() with a version that uses ComplexHeatmap::Heatmap() internally. It also adds support for incorporating the automatic annotation results from annotate_registered_clusters(). NOTE that the max argument was renamed to color_max, as well as min to color_min. Also, the default for min used to be -max and now for color_min the default is the min() correlation observed. The default for max was 0.81 and the default for color_max() is the max() observed correlation.

  • run_app() was also updated to match the updated in layer_stat_cor_plot() and now has 2 new inputs for controlling the annotation process with annotate_registered_clusters(). It also allows downloading a CSV file with the annotation results.

STexampleData

             Changes in version 1.15.2 (2025-03-10)
  • bug fixes: re-built objects Visium_humanDLPFC, Visium_mouseCoronal, Janesick_breastCancer_Chromium, Janesick_breastCancer_Visium

Deprecated and Defunct Packages

SOFTWARE:

Twenty software packages were removed from this release (after being deprecated in Bioc 3.20):

  • ATACCoGAPS, BiocOncoTK, biodbExpasy, biodbKegg, brainflowprobes, BRGenomics, CellaRepertorium, microbiomeMarker, MQmetrics, nanotatoR, netOmics, Pi, polyester, psygenet2r, RandomWalkRestartMH, rDGIdb, Risa, RNAinteract, single, SummarizedBenchmark

  • Please note: HTqPCR, previously announced as deprecated in 3.20, has been updated and remains in Bioconductor.

Thirty nine software packages are deprecated in this release and will be removed in Bioc 3.22:

  • AneuFinder, BEARscc, CBEA, chromstaR, coMET, crossmeta, dce, DeProViR, DIAlignR, Director, erma, GeneGeneInteR, genoCN, gespeR, girafe, GraphPAC, HTSeqGenie, iPAC, MAGeCKFlute, netDx, NeuCA, PanViz, pareg, paxtoolsr, PICS, PING, QuartPAC, RBioinf, ReactomeContentService4R, RGMQL, Rtreemix, SpacePAC, staRank, STdeconvolve, supraHex, synapter, trigger, TypeInfo, zlibbioc

EXPERIMENT DATA:

Two experimental data packages were removed from this release (after being deprecated in BioC 3.20):

  • DmelSGI, RNAinteractMAPK

Three experimental data packages are deprecated in this release and will be removed in Bioc 3.22:

  • benchmarkfdrData2019, parathyroidSE, synapterdata

ANNOTATION DATA:

No annotation packages were removed from this release.

Three annotation packages are deprecated in this release and will be removed in 3.22:

  • mirbase.db, targetscan.Hs.eg.db, targetscan.Mm.eg.db

WORKFLOWS:

No workflow packages were removed from this release.

One workflow package was deprecated in this release:

  • BiocMetaWorkflow

BOOKS:

No books were removed from this release.

No books were deprecated in this release.