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• Bioconductor 3.22 Released

October 30, 2025

Bioconductor:

We are pleased to announce Bioconductor 3.22, consisting of 2361 software packages, 435 experiment data packages, 926 annotation packages, 29 workflows and 6 books.

There are 59 new software packages, 6 new data experiment packages, 2 new annotation packages, no new workflows, 1 new book, and many updates and improvements to existing packages.

Bioconductor 3.22 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.

Note: Currently Bioconductor does not have active daily windows builders. We will be testing the windows binaries generated through the r-universe system. These updated windows binaries will be available shortly after this release. We appreciate your patience as we make them available.

Thank you to everyone for your contribution to Bioconductor.

Visit Bioconductor BiocViews for details and downloads.

Contents

• Getting Started with Bioconductor 3.22
• New Software Packages
• New Data Experiment Packages
• New Annotation Packages
• New Workflow
• New Books
• NEWS from existing software packages
• NEWS from existing data experiment packages
• Deprecated and Defunct Packages

Getting Started with Bioconductor 3.22

To update to or install Bioconductor 3.22:

1. Install R 4.5. Bioconductor 3.22 has been designed expressly for this version of R.

2. Follow the instructions at Installing Bioconductor.

New Software Packages

There are 59 new software packages in this release of Bioconductor.

• anansi Studies including both microbiome and metabolomics data are becoming more common. Often, it would be helpful to integrate both datasets in order to see if they corroborate each others patterns. All vs all association is imprecise and likely to yield spurious associations. This package takes a knowledge-based approach to constrain association search space, only considering metabolite-function pairs that have been recorded in a pathway database. This package also provides a framework to assess differential association.

• anglemania anglemania extracts genes from multi-batch scRNA-seq experiments for downstream dataset integration. It shows improvement over the conventional usage of highly-variable genes for many integration tasks. We leverage gene-gene correlations that are stable across batches to identify biologically informative genes which are less affected by batch effects. Currently, its main use is for single-cell RNA-seq dataset integration, but it can be applied for other multi-batch downstream analyses such as NMF.

• anndataR Bring the power and flexibility of AnnData to the R ecosystem, allowing you to effortlessly manipulate and analyse your single-cell data. This package lets you work with backed h5ad and zarr files, directly access various slots (e.g. X, obs, var), or convert the data into SingleCellExperiment and Seurat objects.

• AWAggregator This package implements an attribute-weighted aggregation algorithm which leverages peptide-spectrum match (PSM) attributes to provide a more accurate estimate of protein abundance compared to conventional aggregation methods. This algorithm employs pre-trained random forest models to predict the quantitative inaccuracy of PSMs based on their attributes. PSMs are then aggregated to the protein level using a weighted average, taking the predicted inaccuracy into account. Additionally, the package allows users to construct their own training sets that are more relevant to their specific experimental conditions if desired.

• batchCorr From the perspective of metabolites as the continuation of the central dogma of biology, metabolomics provides the closest link to many phenotypes of interest. This makes metabolomics research promising in teasing apart the complexities of living systems. However, due to experimental reasons, the data includes non-biological variation which limits quality and reproducibility, especially if the data is obtained from several batches. The batchCorr package reduces unwanted variation by way of between-batch alignment, within-batch drift correction and between-batch normalization using batch-specific quality control samples and long-term reference QC samples. Please see the associated article for more thorough descriptions of algorithms.

• Bioc.gff Parse GFF and GTF files using C++ classes. The package also provides utilities to read and write GFF3 files. The GFF (General Feature Format) format is a tab-delimited file format for describing genes and other features of DNA, RNA, and protein sequences. GFF files are often used to describe the features of genomes.

• blase BLASE is a method for finding where bulk RNA-seq data lies on a single-cell pseudotime trajectory. It uses a fast and understandable approach based on Spearman correlation, with bootstrapping to provide confidence. BLASE can be used to “date” bulk RNA-seq data, annotate cell types in scRNA-seq, and help correct for developmental phenotype differences in bulk RNA-seq experiments.

• CalibraCurve CalibraCurve is a computational tool designed to generate calibration curves for targeted mass spectrometry-based quantitative data. It is applicable to various omics disciplines, including proteomics, lipidomics, and metabolomics. The package also offers functionalities for data and calibration curve visualization and concentration prediction from new datasets based on the established curves.

• CBN2Path CBN2Path package provides a unifying interface to facilitate CBN-based quantification, analysis and visualization of cancer progression pathways.

• cellmig High-throughput cell imaging facilitates the analysis of cell migration across many wells treated under different biological conditions. These workflows generate considerable technical noise and biological variability, and therefore technical and biological replicates are necessary, leading to large, hierarchically structured datasets, i.e., cells are nested within technical replicates that are nested within biological replicates. Current statistical analyses of such data usually ignore the hierarchical structure of the data and fail to explicitly quantify uncertainty arising from technical or biological variability. To address this gap, we present cellmig, an R package implementing Bayesian hierarchical models for migration analysis. cellmig quantifies condition- specific velocity changes (e.g., drug effects) while modeling nested data structures and technical artifacts. It further enables synthetic data generation for experimental design optimization.

• Chromatograms The Chromatograms packages defines an efficient infrastructure for storing and handling of chromatographic mass spectrometry data. It provides different implementations of backends to store and represent the data. Such backends can be optimized for small memory footprint or fast data access/processing. A lazy evaluation queue and chunk-wise processing capabilities ensure efficient analysis of also very large data sets.

• cigarillo CIGAR stands for Concise Idiosyncratic Gapped Alignment Report. CIGAR strings are found in the BAM files produced by most aligners and in the AIRR-formatted output produced by IgBLAST. The cigarillo package provides functions to parse and inspect CIGAR strings, trim them, turn them into ranges of positions relative to the “query space” or “reference space”, and project positions or sequences from one space to the other. Note that these operations are low-level operations that the user rarely needs to perform directly. More typically, they are performed behind the scene by higher-level functionality implemented in other packages like Bioconductor packages GenomicAlignments and igblastr.

• Coralysis Coralysis is an R package featuring a multi-level integration algorithm for sensitive integration, reference-mapping, and cell-state identification in single-cell data. The multi-level integration algorithm is inspired by the process of assembling a puzzle - where one begins by grouping pieces based on low-to high-level features, such as color and shading, before looking into shape and patterns. This approach progressively blends the batch effects and separates cell types across multiple rounds of divisive clustering.

• CSOA Cell Set Overlap Analysis (CSOA) is a tool for calculating per-cell gene signature scores in an scRNA-seq dataset. CSOA constructs a set for each gene in the signature, consisting of the cells that highly express the gene. Next, all overlaps of pairs of cell sets are computed, ranked, filtered and scored. The CSOA per-cell score is calculated by summing up all products of the overlap scores and the min-max-normalized expression of the two involved genes. CSOA can run on a Seurat object, a SingleCellExperiment object, a matrix and a dgCMatrix.

• DeeDeeExperiment DeeDeeExperiment is an S4 class extending the SingleCellExperiment class, designed to integrate and manage omics analysis results. It introduces two dedicated slots to store Differential Expression Analysis (DEA) results and Functional Enrichment Analysis (FEA) results, providing a structured approach for downstream analysis.

• dmGsea The R package dmGsea provides efficient gene set enrichment analysis specifically for DNA methylation data. It addresses key biases, including probe dependency and varying probe numbers per gene. The package supports Illumina 450K, EPIC, and mouse methylation arrays. Users can also apply it to other omics data by supplying custom probe-to-gene mapping annotations. dmGsea is flexible, fast, and well-suited for large-scale epigenomic studies.

• DNEA The DNEA R package is the latest implementation of the Differential Network Enrichment Analysis algorithm and is the successor to the Filigree Java-application described in Iyer et al. (2020). The package is designed to take as input an m x n expression matrix for some -omics modality (ie. metabolomics, lipidomics, proteomics, etc.) and jointly estimate the biological network associations of each condition using the DNEA algorithm described in Ma et al. (2019). This approach provides a framework for data-driven enrichment analysis across two experimental conditions that utilizes the underlying correlation structure of the data to determine feature-feature interactions.

• DOtools This package provides functions for creating various visualizations, convenient wrappers, and quality-of-life utilities for single cell experiment objects. It offers a streamlined approach to visualize results and integrates different tools for easy use.

• DspikeIn Provides a reproducible and modular workflow for absolute microbial quantification using spike-in controls. Supports both single spike-in taxa and synthetic microbial communities with user-defined spike-in volumes and genome copy numbers. Compatible with ‘phyloseq’ and ‘TreeSummarizedExperiment’ (TSE) data structures. The package implements methods for spike-in validation, preprocessing, scaling factor estimation, absolute abundance conversion, bias correction, and normalization. Facilitates downstream statistical analyses with ‘DESeq2’, ‘edgeR’, and other Bioconductor-compatible methods. Visualization tools are provided via ‘ggplot2’, ‘ggtree’, and related packages. Includes detailed vignettes, case studies, and function-level documentation to guide users through experimental design, quantification, and interpretation.

• FinfoMDS F-informed MDS is a new multidimensional scaling-based ordination method that configures data distribution based on the F-statistic (i.e., the ratio of dispersion between groups with shared or differing labels).

• GCPtools Lower-level functionality to interface with Google Cloud Platform tools. ‘gcloud’ and ‘gsutil’ are both supported. The functionality provided centers around utilities for the AnVIL platform.

• goatea Geneset Ordinal Association Test Enrichment Analysis (GOATEA) provides a ‘Shiny’ interface with interactive visualizations and utility functions for performing and exploring automated gene set enrichment analysis using the ‘GOAT’ package. ‘GOATEA’ is designed to support large-scale and user-friendly enrichment workflows across multiple gene lists and comparisons, with flexible plotting and output options. Visualizations pre-enrichment include interactive ‘Volcano’ and ‘UpSet’ (overlap) plots. Visualizations post-enrichment include interactive geneset dotplot, geneset treeplot, gene-effectsize heatmap, gene-geneset heatmap and ‘STRING’ database of protein-protein-interactions network graph. ‘GOAT’ reference: Frank Koopmans (2024) <doi:10.1038/s42003-024-06454-5>.

• gVenn Tools to compute and visualize overlaps between gene sets or genomic regions. Venn diagrams with proportional areas are provided, while UpSet plots are recommended for larger numbers of sets. The package supports GRanges and GRangesList inputs, and integrates with analysis workflows for ChIP-seq, ATAC-seq, and other genomic interval data. It generates clean, interpretable, and publication-ready figures.

• HiCaptuRe Capture Hi-C is a set of techniques that enable the detection of genomic interactions involving regions of interest, known as baits. By focusing on selected loci, these approaches reduce sequencing costs while maintaining high resolution at the level of restriction fragments. HiCaptuRe provides tools to import, annotate, manipulate, and export Capture Hi-C data. The package accounts for the specific structure of bait–otherEnd interactions, facilitates integration with other omics datasets, and enables comparison across samples and conditions.

• HiCPotts The HiCPotts package provides a comprehensive Bayesian framework for analyzing Hi-C interaction data, integrating both spatial and genomic biases within a probabilistic modeling framework. At its core, HiCPotts leverages the Potts model (Wu, 1982)—a well-established graphical model—to capture and quantify spatial dependencies across interaction loci arranged on a genomic lattice. By treating each interaction as a spatially correlated random variable, the Potts model enables robust segmentation of the genomic landscape into meaningful components, such as noise, true signals, and false signals. To model the influence of various genomic biases, HiCPotts employs a regression-based approach incorporating multiple covariates: Genomic distance (D): The distance between interacting loci, recognized as a fundamental driver of contact frequency. GC-content (GC): The local GC composition around the interacting loci, which can influence chromatin structure and interaction patterns. Transposable elements (TEs): The presence and abundance of repetitive elements that may shape contact probability through chromatin organization. Accessibility score (Acc): A measure of chromatin openness, informing how accessible certain genomic regions are to interaction. By embedding these covariates into a hierarchical mixture model, HiCPotts characterizes each interaction’s probability of belonging to one of several latent components. The model parameters, including regression coefficients, zero-inflation parameters (for ZIP/ZINB distributions), and dispersion terms (for NB/ZINB distributions), are inferred via a MCMC sampler. This algorithm draws samples from the joint posterior distribution, allowing for flexible posterior inference on model parameters and hidden states. From these posterior samples, HiCPotts computes posterior means of regression parameters and other quantities of interest. These posterior estimates are then used to calculate the posterior probabilities that assign each interaction to a specific component. The resulting classification sheds light on the underlying structure: distinguishing genuine high-confidence interactions (signal) from background noise and potential false signals, while simultaneously quantifying the impact of genomic biases on observed interaction frequencies. In summary, HiCPotts seamlessly integrates spatial modeling, bias correction, and probabilistic classification into a unified Bayesian inference framework. It provides rich posterior summaries and interpretable, model-based assignments of interaction states, enabling researchers to better understand the interplay between genomic organization, biases, and spatial correlation in Hi-C data.

• HVP HVP is a quantitative batch effect metric that estimates the proportion of variance associated with batch effects in a data set.

• Ibex Implementation of the Ibex algorithm for single-cell embedding based on BCR sequences. The package includes a standalone function to encode BCR sequence information by amino acid properties or sequence order using tensorflow-based autoencoder. In addition, the package interacts with SingleCellExperiment or Seurat data objects.

• igblastr The igblastr package provides functions to conveniently install and use a local IgBLAST installation from within R. IgBLAST is described at https://pubmed.ncbi.nlm.nih.gov/23671333/. Online IgBLAST: https://www.ncbi.nlm.nih.gov/igblast/.

• iModMix The iModMix network-based method offers an integrated framework for analyzing multi-omics data, including metabolomics, proteomics, and transcriptomics data, enabling the exploration of intricate molecular associations within heterogeneous biological systems.

• iscream BED files store ranged genomic data that can be queried even when the files are compressed. iscream can query data from BED files and return them in muliple formats: parsed records or their summary statistics as data frames or GenomicRanges objects, and matrices as matrix, GenomicRanges, or SummarizedExperiment objects. iscream also provides specialized support for importing methylation data.

• linkSet Provides a comprehensive framework for representing, analyzing, and visualizing genomic interactions, particularly focusing on gene-enhancer relationships. The package extends the GenomicRanges infrastructure to handle paired genomic regions with specialized methods for chromatin interaction data from Hi-C, Promoter Capture Hi-C (PCHi-C), and single-cell ATAC-seq experiments. Key features include conversion from common interaction formats, annotation of promoters and enhancers, distance-based analyses, interaction strength metrics, statistical modeling using CHiCANE methodology, and tailored visualization tools. The package aims to standardize the representation of genomic interaction data while providing domain-specific functions not available in general genomic interaction packages.

• LipidTrend “LipidTrend” is an R package that implements a permutation-based statistical test to identify significant differences in lipidomic features between groups. The test incorporates Gaussian kernel smoothing of region statistics to improve stability and accuracy, particularly when dealing with small sample sizes. This package also includes two plotting functions for visualizing significant tendencies in 1D and 2D feature data, respectively.

• looking4clusters Enables the interactive visualization of dimensional reduction, clustering, and cell properties for scRNA-Seq results. It generates an interactive HTML page using either a numeric matrix, SummarizedExperiment, SingleCellExperiment or Seurat objects as input. The input data can be projected into two-dimensional representations by applying dimensionality reduction methods such as PCA, MDS, t-SNE, UMAP, and NMF. Displaying multiple dimensionality reduction results within the same interface, with interconnected graphs, provides different perspectives that facilitate accurate cell classification. The package also integrates unsupervised clustering techniques, whose results that can be viewed interactively in the graphical interface. In addition to visualization, this interface allows manual selection of groups, labeling of cell entities based on processed meta-information, generation of new graphs displaying gene expression values for each cell, sample identification, and visual comparison of samples and clusters.

• markeR markeR is an R package that provides a modular and extensible framework for the systematic evaluation of gene sets as phenotypic markers using transcriptomic data. The package is designed to support both quantitative analyses and visual exploration of gene set behaviour across experimental and clinical phenotypes. It implements multiple methods, including score-based and enrichment approaches, and also allows the exploration of expression behaviour of individual genes. In addition, users can assess the similarity of their own gene sets against established collections (e.g., those from MSigDB), facilitating biological interpretation.

• MetaDICT MetaDICT is a method for the integration of microbiome data. This method is designed to remove batch effects and preserve biological variation while integrating heterogeneous datasets. MetaDICT can better avoid overcorrection when unobserved confounding variables are present.

• miaTime The miaTime package provides tools for microbiome time series analysis based on (Tree)SummarizedExperiment infrastructure.

• MSstatsResponse Tools for detecting drug-protein interactions and estimating IC50 values from chemoproteomics data. Implements semi-parametric isotonic regression, bootstrapping, and curve fitting to evaluate compound effects on protein abundance.

• mutscan Provides functionality for processing and statistical analysis of multiplexed assays of variant effect (MAVE) and similar data. The package contains functions covering the full workflow from raw FASTQ files to publication-ready visualizations. A broad range of library designs can be processed with a single, unified interface.

• notame Provides functionality for untargeted LC-MS metabolomics research as specified in the associated protocol article in the ‘Metabolomics Data Processing and Data Analysis—Current Best Practices’ special issue of the Metabolites journal (2020). This includes tabular data preprocessing and quality control, uni- and multivariate analysis as well as quality control visualizations, feature-wise visualizations and results visualizations. Raw data preprocessing and functionality related to biological context, such as pathway analysis, is not included.

• notameStats Provides univariate and multivariate statistics for feature prioritization in untargeted LC-MS metabolomics research.

• notameViz Provides visualization functionality for untargeted LC-MS metabolomics research. Includes quality control visualizations, feature-wise visualizations and results visualizations.

• omicsGMF omicsGMF is a Bioconductor package that uses the sgdGMF-framework of the \code{sgdGMF} package for highly performant and fast matrix factorization that can be used for dimensionality reduction, visualization and imputation of omics data. It considers data from the general exponential family as input, and therefore suits the use of both RNA-seq (Poisson or Negative Binomial data) and proteomics data (Gaussian data). It does not require prior transformation of counts to the log-scale, because it rather optimizes the deviances from the data family specified. Also, it allows to correct for known sample-level and feature-level covariates, therefore enabling visualization and dimensionality reduction upon batch correction. Last but not least, it deals with missing values, and allows to impute these after matrix factorization, useful for proteomics data. This Bioconductor package allows input of SummarizedExperiment, SingleCellExperiment, and QFeature classes.

• peakCombiner peakCombiner, a fully R based, user-friendly, transparent, and customizable tool that allows even novice R users to create a high-quality consensus peak list. The modularity of its functions allows an easy way to optimize input and output data. A broad range of accepted input data formats can be used to create a consensus peak set that can be exported to a file or used as the starting point for most downstream peak analyses.

• PMScanR Provides tools for large-scale protein motif analysis and visualization in R. PMScanR facilitates the identification of motifs using external tools like PROSITE’s ps_scan (handling necessary file downloads and execution) and enables downstream analysis of results. Key features include parsing scan outputs, converting formats (e.g., to GFF-like structures), generating motif occurrence matrices, and creating informative visualizations such as heatmaps, sequence logos (via seqLogo/ggseqlogo). The package also offers an optional Shiny-based graphical user interface for interactive analysis, aiming to streamline the process of exploring motif patterns across multiple protein sequences.

• SanityR a Bayesian normalization procedure derived from first principles. Sanity estimates expression values and associated error bars directly from raw unique molecular identifier (UMI) counts without any tunable parameters.

• scafari Scafari is a Shiny application designed for the analysis of single-cell DNA sequencing (scDNA-seq) data provided in .h5 file format. The analysis process is structured into the four key steps “Sequencing”, “Panel”, “Variants”, and “Explore Variants”. It supports various analyses and visualizations.

• scGraphVerse A package for inferring, comparing, and visualizing gene networks from single-cell RNA sequencing data. It integrates multiple methods (GENIE3, GRNBoost2, ZILGM, PCzinb, and JRF) for robust network inference, supports consensus building across methods or datasets, and provides tools for evaluating regulatory structure and community similarity. GRNBoost2 requires Python package ‘arboreto’ which can be installed using init_py(install_missing = TRUE). This package includes adapted functions from ZILGM (Park et al., 2021), JRF (Petralia et al., 2015), and learn2count (Nguyen et al. 2023) packages with proper attribution under GPL-2 license.

• scLANE Our scLANE model uses truncated power basis spline models to build flexible, interpretable models of single cell gene expression over pseudotime or latent time. The modeling architectures currently supported are Negative-binomial GLMs, GEEs, & GLMMs. Downstream analysis functionalities include model comparison, dynamic gene clustering, smoothed counts generation, gene set enrichment testing, & visualization.

• Seqinfo The Seqinfo class stores the names, lengths, circularity flags, and genomes for a particular collection of sequences. These sequences are typically the chromosomes and/or scaffolds of a specific genome assembly of a given organism. Seqinfo objects are rarely used as standalone objects. Instead, they are used as part of higher-level objects to represent their seqinfo() component. Examples of such higher-level objects are GRanges, RangedSummarizedExperiment, VCF, GAlignments, etc… defined in other Bioconductor infrastructure packages.

• SETA Tools for compositional and other sample-level ecological analyses and visualizations tailored for single-cell RNA-seq data. SETA includes functions for taxonomizing celltypes, normalizing data, performing statistical tests, and visualizing results. Several tutorials are included to guide users and introduce them to key concepts. SETA is meant to teach users about statistical concepts underlying ecological analysis methods so they can apply them to their own single-cell data.

• shinybiocloader Add a Bioconductor themed CSS loader to your shiny app. It is based on the shinycustomloader R package. Use a spinning Bioconductor note loader to enhance your shiny app loading screen. This package is intended for developer use.

• SmartPhos To facilitate and streamline phosphoproteomics data analysis, we developed SmartPhos, an R package for the pre-processing, quality control, and exploratory analysis of phosphoproteomics data generated by MaxQuant and Spectronaut. The package can be used either through the R command line or through an interactive ShinyApp called SmartPhos Explorer. The package contains methods such as normalization and normalization correction, transformation, imputation, batch effect correction, PCA, heatmap, differential expression, time-series clustering, gene set enrichment analysis, and kinase activity inference.

• SpaceTrooper SpaceTrooper performs Quality Control analysis using data driven GLM models of Image-Based spatial data, providing exploration plots, QC metrics computation, outlier detection. It implements a GLM strategy for the detection of low quality cells in imaging-based spatial data (Transcriptomics and Proteomics). It additionally implements several plots for the visualization of imaging based polygons through the ggplot2 package.

• spARI The R package used in the manuscript “Spatially Aware Adjusted Rand Index for Evaluating Spatial Transcritpomics Clustering”.

• SpectriPy The SpectriPy package allows integration of Python-based MS analysis code with the Spectra package. Spectra objects can be converted into Python MS data structures. In addition, SpectriPy integrates and wraps the similarity scoring and processing/filtering functions from the Python matchms package into R.

• SPICEY SPICEY (SPecificity Index for Coding and Epigenetic activitY) is an R package designed to quantify cell-type specificity in single-cell transcriptomic and epigenomic data, particularly scRNA-seq and scATAC-seq. It introduces two complementary indices: the Gene Expression Tissue Specificity Index (GETSI) and the Regulatory Element Tissue Specificity Index (RETSI), both based on entropy to provide continuous, interpretable measures of specificity. By integrating gene expression and chromatin accessibility, SPICEY enables standardized analysis of cell-type-specific regulatory programs across diverse tissues and conditions.

• STADyUM STADyUM is a package with functionality for analyzing nascent RNA read counts to infer transcription rates. This includes utilities for processing experimental nascent RNA read counts as well as for simulating PRO-seq data. Rates such as initiation, pause release and landing pad occupancy are estimated from either synthetic or experimental data. There are also options for varying pause sites and including steric hindrance of initiation in the model.

• stPipe This package serves as an upstream pipeline for pre-processing sequencing-based spatial transcriptomics data. Functions includes FASTQ trimming, BAM file reformatting, index building, spatial barcode detection, demultiplexing, gene count matrix generation with UMI deduplication, QC, and revelant visualization. Config is an essential input for most of the functions which aims to improve reproducibility.

• SuperCellCyto SuperCellCyto provides the ability to summarise cytometry data into supercells by merging together cells that are similar in their marker expressions using the SuperCell package.

New Data Experiment Packages

There are 6 new data experiment packages in this release of Bioconductor.

• AWAggregatorData The AWAggregatorData package contains the data associated with the AWAggregator R package. It includes two pre-trained random forest models, one incorporating the average coefficient of variation as a feature, and the other one not including it. It also contains the PSMs in Benchmark Set 1~3 derived from the psm.tsv output files generated by FragPipe, which are used to train the random forest models.

• CENTREprecomputed Interface and documentation for the Experiment Hub records needed by the CENTRE Bioconductor software package. The Experiment Hub records contains the precomputed fisher combined p-values, CRUP correlations. Additionally, the records hold ChIP-seq and RNA-seq data used for the example of the software package.

• ChIPDBData Provides curated gene target databases derived from ChIP-seq datasets, formatted as ChIPDB objects for use with TFEA.ChIP.

• DoReMiTra DoReMiTra is an R data package providing access to curated transcriptomic datasets related to blood radiation, with a focus on neutron, x-ray, and gamma ray studies. It is designed to facilitate radiation biology research and support data exploration and reproducibility in radiation transcriptomics. All datasets are provided as SummarizedExperiment objects, allowing seamless integration with the Bioconductor ecosystem.

• iModMixData Provides example datasets for the iModMix package, including gene, protein, and metabolite partial correlation matrices derived from ccRCC4 and FloresData_K_TK studies. The data are preprocessed and ready to use for testing, demonstrating iModMix workflows, and exploring correlation networks.

• nmrdata Provides example one-dimensional proton NMR spectra of murine urine samples collected before and after bariatric or sham surgery (Roux-en-Y gastric bypass). The data are adapted from Jia V Li et al. (2011), “Metabolic surgery profoundly influences gut microbial-host metabolic cross-talk”, Gut, 60(9), 1214–1223. <doi:10.1136/gut.2010.234708>. This package serves as example data for metabolomics analysis and teaching purposes.

New Annotation Packages

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

• CENTREannotation This is an AnnotationHub package for the CENTRE Bioconductor software package. It contains the GENCODE version 40 annotation and ENCODE Registry of candidate cis-regulatory elements (cCREs) version 3. All for Human hg38 genome.

• org.Hbacteriophora.eg.db Provides genome-wide annotation for Heterorhabditis bacteriophora, primarily based on mapping using custom gene identifiers. This OrgDb annotation package is intended for use with AnnotationDbi-based tools and supports querying of gene identifiers and related metadata.

New Workflow Packages

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

New Online Books

There is one new book in this release of Bioconductor.

• OSTA This package contains source files for the “Orchestrating Spatial Transcriptomics Analysis with Bioconductor” online book. This book provides interactive examples and discussion on key principles of computational analysis workflows for spatial transcriptomics data using Bioconductor in R. The book contains chapters describing individual analysis steps as well as extended workflows, each with examples including R code and datasets.

NEWS from existing Software Packages

alabaster.base

                   Changes in version 1.10.0                        

• Bugfix to cloneDirectory() to work with relative/recursive symlinks in the directory to be cloned.

alevinQC

                   Changes in version 1.25.1                        

• Minor fixes to tests to be more robust to possible future changes in ggplot2

AlphaMissenseR

                    Changes in version 1.6.0                        

• (v. 1.5.4) Avoid gghalves in ‘benchmarking’ vignette for compatilibity with updated ggplot2.
• (v. 1.5.4) ensure af_prediction() returns a single entry exactly matching accession number.

AlpsNMR

             Changes in version 4.11.1 (2025-09-24)                 

• Compatibility with ggplot2-4.0.

amplican

                   Changes in version 1.31.2                        

• major changes to amplican way of finding primers, it should be way faster and more robust

• some small fixes to make findLQR more robust

anansi

                   Changes in version 0.99.0                        

Submission to Bioconductor

anglemania

                   Changes in version 0.99.5                        

• Initial submission to Bioconductor.

anndataR

• Initial submission to Bioconductor

AnnotationHub

                   Changes in version 3.99.0                        

MAJOR UPDATES

• 3.99.0 Update downloading method from httr to httr2

BUG CORRECTION

• 3.99.1 Fix bug preventing status message with removeResource

• 3.99.2 Add ability to pass a config argument to download resources

• 3.99.3 Add ability to pass a progress argument to download resources

ATACseqQC

                   Changes in version 1.33.1                        

• add option ‘ATACseqQC.bigFile’

AWAggregator

                   Changes in version 0.99.1                        

• Initial Bioconductor submission

BANDITS

                   Changes in version 1.24.1                        

• ‘create_data’ updated to prevent users from providing an unnamed ‘eff_len’ object;

barbieQ

                    Changes in version 1.1.2                        

• Comment out code that runs bartools functions in vignette.

                    Changes in version 1.1.1                        
  

• Fixed issues in the vignette.

• Fixed bug in the “testBarcodeSignif.R”.

• Added more examples to “testBarcodeSignif.R”.

BASiCS

             Changes in version 2.21.1 (2025-09-17)                 

• Updates divide and conquer approach to use an effect size as a metric to decide whether the partions are balanced (instead of a p-value)

• Minor typos and technical fixes

basilisk

                   Changes in version 1.22.0                        

• Replace conda with PyEnv + virtualenv for Python management and environment creation. This aims to avoid GLIBCXX version errors from mismatches in system libraries between conda and R. Package developers should now directly use PyPI package versions in their packages= specification instead of the conda package versions. Administrators also have more power and flexibility to override the Python instance used by setupBasiliskEnv.

batchCorr

                   Changes in version 0.99.5                        

• Submitted to Bioconductor

BatchQC

                   Changes in version 2.5.14                        

Minor Changes

• Added voom as a normalization method

Bug Fixes

• Corrected limma correction to allow 1 covariate

                   Changes in version 2.5.13                        
  

Major Changes

• Updated Vignette to reflect updates to BatchQC (distribution checks, kBET, UMAP)
• Updated vignette example data to be TB data

Minor Changes

• Updated UMAP example to include covar option

• Changed location of kBET tab

                   Changes in version 2.5.12                        
  

Minor Changes

• Fixed sva batch correction function

• Added covar to UMAP

                   Changes in version 2.5.11                        
  

Major Changes

• Allowed AIC function to take multiple covariates as input

                   Changes in version 2.5.10                        
  

Major Changes

• Added a new kBET tab for measuring batch effect presence

                    Changes in version 2.5.9                        
  

Major Changes

• Added AIC under batch correction tab

                    Changes in version 2.5.8                        
  

Major Changes

• Added svaseq as a batch correction method

                    Changes in version 2.5.7                        
  

Minor Changes

• Added a data onject with subject IDs and BMI info to match the original study with the curatedTBData info and provide missing BMI info

                    Changes in version 2.5.6                        
  

Major Changes

• Added Kruskal-Wallis test as a differential expression analysis method

                    Changes in version 2.5.5                        
  

Major Changes

• Added ANOVA as a differential expression analysis method

                    Changes in version 2.5.4                        
  

Major Changes

• Redesigned tab flow; upload tab reduced, batch correction tab created, and lambda stat and neg binomial distribution check moved to appropriate tabs

Minor Changes

• Updated lambda statistic to provide a recommendation and to check for balanced experimental design
• Abbreviated Normalization usage description

Bug Fix

• Updated “counts” language to “assay” for uploaded data

                    Changes in version 2.5.3                        
  

Major Changes

• Added lambda statistic

Bug Fix

• Corrected log to be log(x+1) and changed CPM(x+1) to CPM(x)

                    Changes in version 2.5.2                        
  

Major Changes

• Added edgeR as a normalization method

• Added edgeR as a differential expression analysis method

                    Changes in version 2.5.1                        
  

Major Changes

• Added TB data example

Minor Changes

• Changed sapply to vapply in nb check

beachmat

                   Changes in version 2.26.0                        

• Added the getExecutor() and Rtatami::set_executor() functions. This ensures that unknown matrices are parallelized safely in downstream packages. Also updated instructions for developers to set the parallel executor in their .onLoad().

bedbaser

                    Changes in version 1.1.1                        

• Update bedbase to 0.10.6
• Update examples
• Remove bigbed

bettr

                    Changes in version 1.5.3                        

• Expand vignette with more details about the app

                    Changes in version 1.5.2                        
  

• Add possibility to specify the default weight for metrics

                    Changes in version 1.5.1                        
  

• Minor fixes to tests to be more robust to possible future changes in ggplot2

Bioc.gff

                   Changes in version 0.99.5                        

• Initial Bioconductor submission.

BiocBaseUtils

                   Changes in version 1.12.0                        

Bug fixes and minor improvements

• The error message from checkInstalled now reports required packages in addition to the installation text.

BiocCheck

                   Changes in version 1.46.0                        

NEW FEATURES

• Checks support qmd vignettes and require that a SystemRequirements field be present and list the quarto CLI in the DESCRIPTION file.

• All chunks in vignettes should have labels (@vjcitn, #222)

• Flag export all regex patterns in NAMESPACE (@lshep, #230)

BUG FIXES AND MINOR IMPROVEMENTS

• Rd pages that do not have \usage sections are excluded from \value checks (@hpages, #225)

• Rd pages that have \keyword{internal} are excluded from \value checks

• Avoid overwritting data document types for \value checks

• Vignettes with no code chunks were incorrectly flagged in chunk label checks

• Chunks in Rnw vignettes with no labels are now correctly identified

• sessionInfo checks in vignettes occur only when code chunks are present

• BiocCheck() options are now ordered alphabetically in documentation to make it easier to find specific options (@Bisaloo, #229).

BiocFileCache

                   Changes in version 2.99.0                        

MAJOR UPDATES

• Update downloading method from httr to httr2

BUG FIX

• (2.99.1) Soft failure for if HEAD does not work. Will still download and add to cache without caching information. Additionally fix bug so config can be passed down to HEAD call from bfcneedsupdate, bfcadd, and bfcrpath.

• (2.99.4) Fix bug to pass proxy down to HEAD call

NEW FEATURE

• (2.99.2) Add progress argument to bfcadd/bfcdownload to control if a progress bar is displayed during an interactive session

BiocGenerics

                   Changes in version 0.56.0                        

BUG FIXES

• Fix updateObject() infinite recursion on an environment that contains itself.

• Small tweak to updateObject(<data.frame>).

BiocNeighbors

                    Changes in version 2.4.0                        

• Updated the C++ interfaces to match updates to the underlying knncolle libraries.

BioCor

                    Changes in version 1.34                         

• Remove example on vignettes with deprecated package targetscan.Hs.eg.db
• Fix documentation issue
• Fix deprecation message related to testthat 3rd edition.

BiocParallel

                    Changes in version 1.44                         

TRANSFERRING MAINTAINERSHIP

• (1.43.4) Transfer maintainership to Jiefei Wang

NEW FEATURES

• (1.43.2) Lazy-load S4 classes in workers; see https://github.com/Bioconductor/BiocParallel/issues/262 https://github.com/Bioconductor/BiocParallel/pull/270

• (1.43.1) Support NULL return value from bplapply; see https://github.com/Bioconductor/BiocParallel/issues/267 https://github.com/Bioconductor/BiocParallel/pull/269

BiocPkgTools

                   Changes in version 1.28.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• biocVIEWSdb parses the package metadata VIEWS file

• pkgBiocRevDeps now has recursive argument

• repositoryStats supports in-house repositories with local=TRUE

• The dependency report template now uses pkgndep to display a dependency heatmap

BUG FIXES AND MINOR IMPROVEMENTS

• Enhance summary method for biocrevdeps class output from pkgBiocRevDeps

biocViews

                   Changes in version 1.77.2                        

ENHANCEMENT

• (1.77.2) Add build_db_from_source, build_meta_aliases_db, build_meta_rdxrefs_db

• (1.77.3) Add biocViews term GPU

biomaRt

                   Changes in version 2.66.0                        

BREAKING CHANGES

• the https argument in useEnsembl() has been removed, as announced in version 2.50.0. Connections to Ensembl mirrors now always use https://, as enforced by a redirect from the server.

USER VISIBLE CHANGES

• This package documentation is now available as a pkgdown website at https://huber-group-embl.github.io/biomaRt/.

• The exportFASTA() function is now roughly 5x faster.

BUG FIXES

• getGene() no longer errors with “This function only works when used with the ensembl BioMart.”, that was always returned, even when using the ensembl BioMart. This bug was introduced in version 2.27.1 (Bioconductor 3.3). Thanks to Tobias Hoch for the report.

• This package now explicitly depends on R >= 4.1.0. This was effectively already the case since version 2.58, in line with Bioconductor policy, but not explicitly documented in DESCRIPTION.

• getBM() no longer silently convert alleles “T” and “F” to logical TRUE and FALSE. This rarely happened when a single allele, coincidentally named “T” or “F”, was returned in a column. Thanks to Sina Rüeger for the report.

• getBM() now internally handles redirects and automatically resubmits the query to the new location. This fixes issues when using versioned forms such as https://eg59-plants.ensembl.org/, which redirects to https://may2024-plants.ensembl.org/index.html. Thanks to Edoardo Bertolini for the report.

INTERNAL CHANGES

• Coding style throughout the package has been harmonized using the air tool. Contributors using RStudio, Positron or VS Code should have their code styled automatically on save.

• A duplicated definition of the .getEnsemblSSL() internal function has been removed.

• Static analysis via the lintr package is now performed on each push and PR. It should mostly be invisible to users but might result in slightly increased performance in some cases.

• This package now uses roxygen2 to generate documentation and NAMESPACE.

• A R CMD check NOTE about a missing import has been resolved.

• This package continuous integration setup now errors on R CMD check WARNINGs. This is checked on each push and PR.

• The digest and rappdirs dependencies have been removed in favour of functions provided by the base R tools package.

• Examples have been reviewed and fixed where necessary.

• testthat edition 3 (instead of previously edition 2) is now used for unit tests.

biosigner

                   Changes in version 1.37.4                        

MINOR MODIFICATION

• minor documentation update

                   Changes in version 1.37.2                        
  

MINOR MODIFICATION

• SpikePos dataset from the BioMark package now included in biosigner

Biostrings

                   Changes in version 2.78.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• The package now depends on Seqinfo instead of GenomeInfoDb.

DEPRECATED AND DEFUNCT

• All the functions that went to the pwalign package in BioC 3.19 and got formally deprecated in Biostrings in BioC 3.21 are now defunct.

• After being deprecated in BioC 3.19, XStringPartialMatches objects and matchprobes() are now defunct.

• Remove needwunsQS() (was defunct in BioC 3.19).

BUG FIXES

• Fix: minor bug with input verification in write.phylip; clean up formatting (#124). By Aidan Lakshman.

blase

                    Changes in version 1.0.0                        

• Initial release.

BreastSubtypeR

                    Changes in version 1.1.8                        

Highlights

• Paper published in NAR Genomics and Bioinformatics (2025), Editor’s Choice (DOI: 10.1093/nargab/lqaf131).
• Support for raw RNA-seq counts (requires gene lengths).
• iBreastSubtypeR refresh: cleaner UX, smarter AUTO guidance, consistent exports.
• Refined, data-driven thresholds for ER/HER2 skew detection in AUTO.
• Broader input-validation across the subtyping pipeline.

Bug Fixes

• AUTO: fixed ER/HER2 strata messaging for ER+/HER2− and ER−/HER2− cohorts. The spurious message “ssBC.v2 for samples: ERnegHER2neg” no longer appears in ER+/HER2− cohorts.
• AUTO: in pure HER2+ cohorts, ssBC.v2 is now preferred as intended; ssBC is not listed or subset-indexed there.
• AUTO: ssBC / ssBC.v2 sample-subsetting and messages now occur only when that method is actually selected.
• PAM50 variants no longer error with calibration = “None” or “External”.
• ssBC variants handle datasets with <50 PAM50 genes more robustly.
• Fixed data.frame issue (“check.names matched by multiple arguments”) via safe builders.
• Removed duplicate “Subtype == BS_*class” columns in downloads.
• Safer ROR merges on PatientID with clearer notifications.
• Eliminated jsonlite named-vector warning in plotting.

Changes

• Documentation: clarified guidance for subtype-specific cohorts:
• ER/HER2-defined cohorts (ER+/HER2−, ER−/HER2−, ER+/HER2+, ER−/HER2+): NC-based → ssBC.v2 only; plus SSP-based (AIMS, sspbc).
• ER-only (ER+ or ER−) and TNBC: NC-based → ssBC and/or ssBC.v2 (subject to minimum sizes); plus SSP-based.
• AUTO clarifications (simulation-based defaults):
• ER balance gate: lower_ratio = 0.39, upper_ratio = 0.69.
• Minimum sizes: ER+ total = 15, ER− total = 18, TN total = 18.
• Subgroup gates (rounded): ER+ subgroups (HER2+ / HER2−) use round(15 / 2); ER− subgroups (HER2+ / HER2−) use round(18 / 2).
• Notes: these thresholds gate method eligibility; they do not force a consensus call. Details in the vignette (“AUTO logic”).

Shiny (iBreastSubtypeR)

• New hero card + method chips (NC, SSP, ROR, AUTO) and “Why AUTO?” explainer modal.
• AIMS: 4-class toggle disabled (AIMS is 5-class only).
• AUTO/AIMS/SSPBC: Full-metrics export selector hidden.
• Clear per-method help + PAM50 calibration notes.
• Small UX polish: file dialogs + Mapping preserve scroll position.

Exports

• Two modes: Calls only and Full metrics (incl. ROR when available).
• Standard column names: Call_5class / Call_4class (internal BS / BS.Subtype mapped).
• AUTO: Calls = selected-k table (+ entropy); Full = selected-k merged with other-k (suffix _4class / _5class).
• Filenames encode method, class, and mode (e.g., results-PAM50-5class-full.txt).

Behavior & Validation

• ROR only for NC methods when TSIZE/NODE exist and are numeric (auto coercion + warnings).
• Stricter checks for ssBC subgroups (ER/HER2/TN presence and coding).
• AUTO preflight warns on missing or mis-coded ER/HER2.

Core Features (unchanged)

• Unified NC (PAM50, cIHC, PCAPAM50, ssBC) and SSP (AIMS, SSPBC) subtyping under one API.
• BS_Multi with cohort-aware AUTO selection; Mapping for platform-agnostic preprocessing.
• Interactive Shiny app with Bioconductor-friendly exports.

Upgrade Notes

• Raw RNA-seq counts are supported from v1.1.3 onward (requires gene lengths).
• If you previously parsed BS / BS.Subtype, switch to Call_5class / Call_4class.
• Package API unchanged.

BridgeDbR

                   Changes in version 2.19.3                        

BUG FIXES

• Sorts the vignette to list the tutorial first

                   Changes in version 2.19.2                        
  

BUG FIXES

• Better package install instructions in the new secondary vignette

                   Changes in version 2.19.1                        
  

NEW FEATURES

• Added a compact resource identifier example to the vignette
• Added a second vignette explaining how sec2pri identifier mappings databases can be used

BUG FIXES

• Handle Bioregistry.io ChEBI compact identifiers better

BSgenome

                   Changes in version 1.78.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• The package now depends on the new Seqinfo package instead of GenomeInfoDb.

BSgenomeForge

                   Changes in version 1.10.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Add Seqinfo to Depends.

BUG FIXES

• Make sure internal helper create_2bit_BSgenome_datapkg() can move the 2bit file across partitions without getting hit by an “Invalid cross-device link” error.

CAGEr

                   Changes in version 2.16.0                        

NEW FEATURES

• Pass normalised expression values to quickEnhancers(). Closes #132.
• New correlationMatrix() function to compute correlation matrix without plotting it. Closes #129.
• Save power law alpha value in the reference.slope element of the meta slot of the ggplot2 object produced by plotReverseCumulatives().
• Support for importing CTSS data from bigWig files.

BUG FIXES

• Stop passing StitchedGPos to quickEnhancesr(). Closes #133.
• Migrate from GenomeInfoDb to Seqinfo where needed.

CalibraCurve

                   Changes in version 0.99.0                        

Initial submission to BioConductor.

CAMERA

                   Changes in version 1.65.1                        

BUG FIXES

• Fix a few more logic expressions causing “the condition has length > 1” type issues

Cardinal

             Changes in version 3.11.1 (2025-10-14)                 

NEW FEATURES

• Added ‘contrastTest()’ method for post-hoc contrasts on ‘MeansTest’ objects

• New ‘ContrastTest’ class for storing contrast analysis results

• Added support for ‘use_lmer=TRUE’ in ‘meansTest()’ to use lmerTest::lmer

• Integration with ‘emmeans’ package for estimated marginal means and contrasts

• Support for various contrast methods: pairwise, trt.vs.ctrl, custom contrasts

• Added ‘emm_adjust’ parameter for multiple comparison adjustments

SIGNIFICANT USER-VISIBLE CHANGES

• When ‘use_lmer=TRUE’ in ‘meansTest()’, likelihood ratio tests are not performed; use ‘contrastTest()’ for post-hoc comparisons instead

• Suggests ‘lmerTest’ and ‘emmeans’ packages for enhanced functionality

CatsCradle

                    Changes in version 1.3.3                        

• Example data ligandReceptorResults.rda saved in compressed format.

                    Changes in version 1.3.2                        
  

• Function getLigandReceptorPairsInPanel rewritten for faster runtime.
• Analytical option to calculate pvalues added to computeNeighbourEnrichment. This has a faster runtime.
• Function performLigandReceptorAnalysis rewritten for faster runtime by making use of sparse matrices.
• Analytical option to calculate pvalues added to performLigandReceptorAnalysis. This has a faster runtime.

• Function plotLRDotplot added to visualise ligand-receptor interactions returned by performLigandReceptorAnalysis.

                    Changes in version 1.3.1                        
  

• smallXenium@images$fov@misc = list() field added to smallXenium example data for compatability with Seurat updates.

cBioPortalData

                   Changes in version 2.22.0                        

New features

• Defunct removeDataCache for cBioPortalData as caching mechanism is no longer used. Run cBioCache() to get the cache location for deletion. Note that cBioDataPack will continue to cache data files at that location.

cellmig

                   Changes in version 0.99.14                       

• Initial submission to Bioconductor

cellxgenedp

                    Changes in version 1.13                         

BUG FIXES

• (v. 1.12.1 / 1.13.1) Do not attempt to ‘unlist’ any facet column in datasets or collections

ceRNAnetsim

             Changes in version 1.21.0 (2025-08-10)                 

• ggplot2 uses a new class of the objects, do some tests were deprecated.
• The citation errors were fixed.

chevreulPlot

• Initial Bioconductor submission

chevreulProcess

• Initial Bioconductor submission

chevreulShiny

• Initial Bioconductor submission

ChIPpeakAnno

                   Changes in version 3.43.2                        

• Fix an issue for the corrdinates changes of GRCh37 annotation.

                   Changes in version 3.43.1                        
  

• Fix an issue in genomicElementDistribution when convert seqlevelsStyle.

ChIPseeker

                   Changes in version 1.45.2                        

• new cache mechanism from ‘yulab.utils’ (2025-10-15, Wed)

Chromatograms

• Initial Bioconductor submission

CircSeqAlignTk

             Changes in version 1.11.2 (2025-05-09)                 

SIGNIFICANT USER-VISIBLE CHANGES

• Remove get_slot_contents function. Use slot function instead.

• Change default aligner to HISAT2 from Bowtie2.

• Change repository.

• Update documentation.

ClassifyR

                   Changes in version 3.14.0                        

• Precision pathways gains an all-combinations-of-all-subsets mode.

cleaver

             Changes in version 1.47.1 (2025-10-14)                 

• Move package to codeberg.org.

ClustIRR

                    Changes in version 1.7.7                        

• Bugfix, model improvement

                    Changes in version 1.7.3                        
  

• Function for quantifying community purity wrt node features

ComplexHeatmap

                   Changes in version 2.25.2                        

• make_layout,HeatmapList-class: row_order/column_order is reset if cluster_rows/cluster_columns is set to TRUE in draw().

                   Changes in version 2.25.1                        
  

• adjust_heatmap_list(): fixed a bug where slice gaps were repeatedly used to calculate the heatmap width/height. #1240

• names<-,HeatmapAnnotation(): label slot is correctedly assigned with the new name.

consensusSeekeR

                   Changes in version 1.37.3                        

SIGNIFICANT USER-VISIBLE CHANGES

• The package documentation has been updated.

Coralysis

                    Changes in version 0.99.0                        

First release:

• Functions:
• AggregateDataByBatch()
• RunParallelDivisiveICP()
• ReferenceMapping()
• GetCellClusterProbability()
• SummariseCellClusterProbability()
• CellClusterProbabilityDistribution()
• BinCellClusterProbability()
• TabulateCellBinsByGroup()
• CellBinsFeatureCorrelation()
• FindClusterMarkers()
• FindAllClusterMarkers()
• MajorityVotingFeatures()
• RunPCA()
• RunTSNE()
• RunUMAP()
• PCAElbowPlot()
• PlotDimRed()
• PlotExpression()
• PlotClusterTree()
• VlnPlot()
• HeatmapFeatures()
• PrepareData()
• GetFeatureCoefficients()
• Vignettes:
• Integration
• Reference-mapping
• Cell States

COTAN

                    Changes in version 2.9.7                        

Fixed underflow error appearing when the dispersion is very small

Improved the test.dataset to be somewhat more realistic

                    Changes in version 2.9.6                        

Upgraded dispersion solver to use Newton-Raphson method Minor variations of the model parameters are expected

Improved the torch coex code so to use less memory and do less calculations

                    Changes in version 2.9.5                        

Reduced significantly the memory foot-print while use multi-process solvers Also improved speed of GDI and data-reduction calculations, by going multi-process there too

Improved function cellsUniformClustering() mechanism in case of larger datasets when resolution ceiling was causing unnecessary slowdown and in cases early termination too

                    Changes in version 2.9.4                        

Solved minor issue with maxIterations argument in the function cellsUniformClustering(): it was doing two extra loops

Fixed bug with function isCoexAvailable() when used with COTAN objects created with older versions

                    Changes in version 2.9.3                        

Fixed issue with function getSelectedGenes() in cases when asked for HGDI selection and dataset GDI is low overall: it was returning too few and, in some cases, even no genes

Added possibility to choose which data matrix to use for clusterizations and UMAP plots. Also now it is possible to use a projection onto the main COEX matrix eigen-vectors as alternative to the PCA as dimensionality reduction tool

                    Changes in version 2.9.2                        

Solved issues with breaking changes from zeallot package

Expanded calculateLikelihoodOfObserved() to support more formulas related to likelihood

Unified code that produces UMAP plots: now they all run UMAPPlot() that in turn calls the Seurat::RunUMAP() function

Fixed issue with use of parallelDist::parDist() on Linux aarch64 machines: it crashed irrecoverably due to an invalid alignment error. Now code calls the normal dist() function on such machines

                    Changes in version 2.9.1                        

Solved issue with reordering of merged clusterization: flag keepMinusOne was off and label “-1” was moved around

Added checker class type to the data.frame obtained after conversion. It will make loading checker results from file easier

Improved README.md with stable links to devel and release versions in BioConductor

countsimQC

                   Changes in version 1.27.1                        

• Minor maintenance updates

CPSM

                    Changes in version 1.1.4                        

Updates

• Updated Lasso_PI_scores_f.R, MTLR_pred_model_f.R, Univariate_sig_features_f.R, km_overlay_plot_f.R, mean_median_surv_barplot_f.R, surv_curve_plots_f.R, predict_survival_risk_group_f.R to provide customization for user in cross-validation , Font-size and figure styling etc.
• Updated MTLR_pred_model_f.R to compute IBS (integrated brier score)
• Updated vignettes/CPSM.Rmd to provide improve description and workflow
• Updated tests/testthat files to incoprate updated changes
• Updated DESCRIPTION file:

• Bumped version from 1.1.3 to 1.1.4.

                    Changes in version 1.1.3                        
  

Updates

• Added CC0 license for processed data in the /data folder to comply with data-sharing requirements.
• Updated km_overlay_plot_f.R to improve figure
• Updated DESCRIPTION file:
• Added contributors (ctb) to Authors@R.

• Bumped version from 1.1.2 to 1.1.3.

                    Changes in version 1.1.2                        
  

##Improvement

• Updated MTLR_pred_model_f.R, Lasso_PI_scores_f.R, mean_median_surv_barplot_f.R, Nomogram_generate_f.R,surv_curve_plots_f.R script to remove undesired package
• Updated km_overlay_plot_f.R to improve figure
• Updated DESCRIPTION file include required biocview terms

Version update

• Bumped version from 1.1.1 to 1.1.2.

                    Changes in version 1.1.1                        
  

##Improvement

• Updated MTLR_pred_model_f function to make it simple

Version update

• Bumped version from 1.1.0 to 1.1.1.

                    Changes in version 1.1.0                        
  

New Features

• predict_survival_risk_group_f():
• Added a new function to build Random Forest-based survival risk group classifiers using selected molecular features.
• Automatically selects the best-performing model based on prediction accuracy across various ntree values (10 to 1000).
• Outputs include predicted risk groups, prediction probabilities, misclassification summary, best model, and tree-wise performance matrix.
• km_overlay_plot_f():
• Introduced a new function to generate Kaplan-Meier survival plots overlayed with individual test sample survival curves.
• Useful for visualizing predicted test sample risk in the context of population-level survival groups.
• Includes annotated output with sample ID, predicted group, and probability.

Updated data files, added new files

Improvement

• Updated MTLR_pred_model_f function to compute MAE and improve the structure of function.

Documentation

• Updated Description file
• Updated vignette file CPSM.Rmd:
• Included usage details and examples for new functions.
• Enhanced step-by-step explanation of prediction and visualization workflows.

Version update

• Bumped version from 1.0.0 to 1.1.0

crisprBase

                   Changes in version 1.13.2                        

• Added PAM weights to the SPG nuclease.

                   Changes in version 1.13.1                        
  

• Added the option of not scaling editing weights in BaseEditor function.

crumblr

                    Changes in version 1.0.7                        

• Feb 1, 2022
• fix vst()
• add plots plotScatterDensity() and meanSdPlot() for VST

• add vignette vst.Rmd

                    Changes in version 1.0.6                        
  

• Jan 31, 2022

• add logo, example data

                    Changes in version 1.0.5                        
  

• Dec 27, 2021
• add dmn.mle()

• use generic crumblr() function

                    Changes in version 1.0.4                        
  

• Dec 23, 2021
• Update vignette

• export clr()

                    Changes in version 1.0.3                        
  

• Dec 20, 2021

• fix vst bug

                    Changes in version 1.0.2                        
  

• Dec 20, 2021

• add vst

                    Changes in version 1.0.1                        
  

• Oct 29, 2021
• handle data.frame

CSOA

             Changes in version 0.99.0 (2025-07-12)                 

• Submitted to Bioconductor

CTexploreR

                     Changes in version 1.5                         

CTexploreR 1.5.2

• Remove documentation for internal functions.

CTexploreR 1.5.1

• Move some tests to longtests.

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

CytoPipeline

                     Changes in version 1.9                         

CytoPipeline 1.9.4

• improved aggregateAndSample() added a setup parameter, such that when it is equal to “forceNEvent”, the nb of events selected per flow frame is not always balanced, to always obtain nTotalEvents (except when the total nb of available events, taking all flowFrames, is less than nTotalEvents).

CytoPipeline 1.9.3

• added sampleDisplayNames()

CytoPipeline 1.9.2

• sample files can now have duplicate base names (provided full paths are different)
• pData<- is now more liberal.

1. It can accept new pData containing more rows than existing sample names (the corresponding subset of pData is taken).
2. It can accept pData with row names pointing to either sample file full paths or base file names
3. It can accept pData with no row names provided the number of rows correspond to the number of sample files. Row names are then set by default to sample file base names (if unique), or sample file full paths.

CytoPipeline 1.9.1

• upgraded to GHA cache v4

CytoPipelineGUI

                     Changes in version 1.7                         

CytoPipelineGUI 1.7.2

• using sample display names instead of base names or full paths, as provided from CytoPipeline 1.9.3

CytoPipelineGUI 1.7.1

• migrated to GHA cache v4

dar

                    Changes in version 1.5.3                        

Bug Fixes

• https://github.com/MicrobialGenomics-IrsicaixaOrg/dar/issues/117

DeconvoBuddies

                    Changes in version 1.1.5                        

BUG FIXES

Correct (est_prop/est_prop_test) data usage after changes in v1.1.4

                    Changes in version 1.1.4                        

BUG FIXES

Package BisqueRNA is no longer a suggested dependency (no longer available on CRAN).

Vignette “Deconvolution Benchmark in Human DLPFC” now loads pre-computed est_prop data instead of running Bisque deconvolution.

                    Changes in version 1.1.3                        

NEW FEATURES

• plot_gene_express() now has the option to use “free_y” axis.

                    Changes in version 1.1.2                        
  

NEW FEATURES

• plot_gene_express() now has the option to change plot_type to ‘violin’ or ‘boxplot’

                    Changes in version 1.1.1                        
  

BUG FIXES

• get_mean_ratio() was initially coercing sparse matrices into in memory matrices. We resolved this by using MatrixGenerics::rowMeans() and MatrixGenerics::rowMedians(). This issue was reported by @cyntsc.

DeeDeeExperiment

• Initial Bioconductor Submission

deepSNV

             Changes in version 1.99.3 (2013-07-25)                 

Updates

• A few changes to shearwater vignette

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

Bugfixes

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

             Changes in version 1.99.2 (2013-07-11)                 
  

Updates

• Updated CITATION

• Added verbose option to bam2R to suppress output

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

Bugfixes

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

             Changes in version 1.99.1 (2013-06-25)                 
  

Updates

• Using knitr for prettier vignettes

• Including shearwater vignette

Bugfixes

• fixed issues with deletions in bf2Vcf()

• makePrior() adds background on all sites

             Changes in version 1.99.0 (2013-04-30)                 
  

Updates

• New shearwater algorithm

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

DEGreport

                   Changes in version 1.45.1                        

• Fixed labs() function calls in multiple R files:
  • methods.R (2 occurrences in degMean and degVar functions)
  • clustering.R (2 occurrences)
  • volcanoPlot.R (1 occurrence)

DelayedArray

                   Changes in version 0.36.0                        

DEPRECATED AND DEFUNCT

• Get rid of SparseArraySeed objects, OLD_extract_sparse_array(), and read_sparse_block(). These were deprecated in BioC 3.20 and defunct in BioC 3.21.

DEP

                   Changes in version 1.31.1                        

• Fixed broken documentation links to Msnbase impute methods.

• Fixed crash at the launch of the shiny apps.

DESeq2

                   Changes in version 1.50.0                        

• New method UPSHOT for lfcThreshold/altHypothesis.

• Fixes for lesser-used functionality, e.g. useT, weights with numeric contrast and the SE computation, summary printing. CHANGES IN VERSION 1.49.6

• Fixes for combined use of useT and greaterAbs in results(), thanks to a PR from Raphael (@rrross)

                   Changes in version 1.49.4                        
  

• The wrong weights matrix was being used when recomputing the SE within results() for the numeric-style contrast. Fixed.

• glmGamPoi and parallel error instead of warning.

                   Changes in version 1.49.1                        
  

• Resolving an issue where lfcThreshold was changed to 0 in the summary() print-out after lfcShrink() even if s-values were not computed.

DFplyr

                    Changes in version 1.4.0                        

NEW FEATURES

• [ and rbind methods now respect groups
• Added left_join(), right_join(), inner_join(), and full_join()

SIGNIFICANT USER-VISIBLE CHANGES

• rename2 deprecated; rename is now a DataFrame method on S4Vectors generic

dittoSeq

                   Changes in version 1.21.1                        

• Minor changes to ensure compatibility with ggplot2 version 4.0.0 changes. Notably, the ‘MASS’ package is now added as a suggested companion package, and error messages suggesting its installation were added for features which rely on functionality from this package. This change is concurrent with ggplot2 itself downgrading the tool from an imported requirement to a suggested addition.
• Minor changes to ensure compatibility with ComplexHeatmap in how the ‘drop_levels’ input of ‘dittoHeatmap()’ is handled. See function documentation for details.

dmGsea

                    Changes in version 0.99                         

• Initial release to Bioconductor.

DMRcaller

Changes in Version 1.42.1:

• Added functions to read Oxford Nanopore methylation data from Dorado bam files
• Added functions to detect Partially Methylated Domains PMDs
• Added functions to detect Variably methylated domains (VMDs) using ONT data
• Added functions to detect Variably Methylated Regions (VMRs) using ONT data
• Added functions to detect co-methylation using ONT data
• Updated parallel computing to use BiocParallel

DOtools

• Initial submission to Bioconductor

DropletUtils

                   Changes in version 1.30.0                        

• Further improvements to the knee point detection in barcodeRanks(). This now uses a curve-tracing algorithm where the knee is defined inside the window with the highest curvature. We also refine inflection point to report the earlier location if multiple inflection points are present on the curve.

• Improve the efficiency of Matrix Market file parsing in read10xCounts(). We support multi-threaded parsing and can directly read into dgCMatrices or SVT_SparseMatrices without intermediate. This is based on the eminem C++ library from the assorthead package.

DspikeIn

• Initial submission to Bioconductor

DuplexDiscovereR

                    Changes in version 1.3.4                        

• Date: 2025-09-29

• Added experimental functionality for prioritisation of ambiguous annotation to annotateGi()

                    Changes in version 1.3.1                        
  

• Date: 2025-07-04
• Added trimming of the PE alignments relative to the ligation point.
• For the PE reads processed by STAR, the type of the junction is detected.
• To narrow down the hybrid prediction, user can trim reads - N_trim nt will be left adjacent to the ligation point.
• Added missing arguments to the function runDuplexDiscoverer which runs the whole pipeline. Keys for annotation features, trimming and minimum chimeric length cutoffs have defaults, also can be set by user to be passed to the functions called from inside the runDuplexDiscoverer.

dupRadar

                   Changes in version 1.39.1                        

• Feature: add tmpDir parameter to analyzeDuprates (credit: Adam Talbot) Resolves performance issues on FUSE-based filesystems by allowing temporary files to be written to fast local storage instead of CWD

edgeR

             Changes in version 4.8.0 (2025-10-01)                  

• The adaptive.span argument of voomLmFit() is now set to TRUE by default, meaning that the span is chosen by chooseLowessSpan().

• The default value of span for estimateDisp() and WLEB() is now chosen by chooseLowessSpan().

• New function catchOarfish().

• New argument path for catchRSEM().

• glmTreat() no longer writes a message about switching to glmLRT() when lfc=0.

• Revise help page for diffSplice.DGEGLM().

• Revise help page for filterByExpr().

eisaR

                   Changes in version 1.21.1                        

• various code improvements detected by lintr

ELViS

                   Changes in version 1.1.12                        

• Minor bug fix in test script

                   Changes in version 1.1.11                        
  

• Added error handling code regarding conda env creation error

                   Changes in version 1.1.10                        
  

• Reflected changes made in 1.1.9 to test scripts

• If conda env creation fails in samtools_reticulate mode, it defaults to Rsamtools for base-level read depth calculation.

                    Changes in version 1.1.9                        
  

• Using reticulate to install and use conda environment

                    Changes in version 1.1.8                        
  

• Fixed some incompatibility issue with basilisk package. basilisk does not support conda package installation at least for now. So partly reverted to reticulate package for samtools installation.

                 Changes in version 1.1.1-1.1.7                     
  

• Build error fix

                    Changes in version 1.1.0                        
  

• Released in Bioconductor

EnrichmentBrowser

                   Changes in version 2.40.0                        

• getGenesets now supports MSigDB’s new designated mouse collections named ‘MH’ (hallmark), ‘M1’(genomic position), ‘M2’ (curated databases), and so on.

enrichplot

                   Changes in version 1.29.4                        

• remove deprecated aes_string/aes_ (2025-10-23, Thu, #332)

                   Changes in version 1.29.3                        
  

• bug fixed of cnetplot for CompareClusterResult (2025-09-13, Sat, #329)
• color gene according to the gene cluster info

• bug fixed in pie scale label (2025-07-14, Mon, #328)

                   Changes in version 1.29.2                        
  

• update treeplot with two parameters, leave_fontsize and clade_fontsize (2025-07-12, Sat, #324, #325)
• remove the fontsize parameter as it only works for clade_fontsize
• ‘log10’ transform for pvalue color scale by default (2025-07-12, Sat, #316)
• introduce new parameters in gseaplot2() (2025-07-12, Sat)
• pvalue_table_columns
• pvalue_table_rownames

• https://github.com/YuLab-SMU/clusterProfiler/issues/774

                   Changes in version 1.29.1                        
  

• throw error in goplot() if ontology is not one of the ‘MF’, ‘CC’ or ‘BF’ (2025-04-28, Mon, clusterProfiler#768)

enrichViewNet

                    Changes in version 1.7.3                        

NEW FEATURES

• The new functions createBasicEmapAsIgraph(), createEnrichMapMultiBasicAsIgraph(), generates enrichment maps in an igraph format.

                    Changes in version 1.7.2                        
  

BUG FIXES AND IMPROVEMENTS

• All functions using ggplot2 are using updated ggplot2 functions.

                    Changes in version 1.7.1                        
  

BUG FIXES

• The package uses a fixed version of gprofiler database in the unit tests.

ensembldb

                   Changes in version 2.33.2                        

• Update description to create EnsDb databases using the docker image.

EpiCompare

                   Changes in version 1.13.2                        

Bug Fixes

• [BREAKING CHANGE] Temporarily disable upset_plot option as one of the dependencies, ComplexUpset, is not yet updated to support ggplot 4.4.0.
• Fix deprecated ggplot arguments.

Miscellaneous

• add_download_button:
• No longer changes to TRUE if run_all is TRUE.

EpipwR

                    Changes in version 1.3.2                        

Major updates

• Users now have the ability to provide custom methylation data
• Users now have the ability to specify a non-normal distribution for phenotype data
• A new function is available for pwrEWAS users to “translate” a pwrEWAS distribution of effect sizes into EpipwR parameters. Please note that all pwrEWAS effect size distributions are truncated normal distributions centered at 0

epiregulon

                    Changes in version 2.0.0                        

• New function in the workflow, optimizeMatacellNumber, which estimates the optimal value of the cellNum parameter passed to calculateP2G.
• Using scrapper::clusterKmeans to implement deterministic algorithm of determination k-mean cluster. It is used to create metacells in the calculateP2G function.
• Added to the output of calculateP2G function empirical p-values and FDR. The null distribution is calculated based on random links of peaks to the genes from other chromosomes.
• Default ChIP-seq output from tfBinding is changed to version 2 which imposes more stringent cutoffs. We have increased the number of unique reads to 20M (previously 10M in version 1) and the number of peaks passing FDR < 1e-5 to 1000 peaks (previously 100 peaks in version 1). For ENCODE data, we now remove any samples with Audit.NOT_COMPLIANT or Audit.ERROR. Flags.
• The argument method to calculateActivity has been deprecated.

• Bug corrected in addLogFC. p-values were mistakenly transformed from log10 when it should be transformed from natural log when logFC_ref or/and logFC_condition was specified

                    Changes in version 1.5.1                        
  

• checking for the duplicated gene names in the input gene expression SingleCellExperiment
• validation of the regulon object passed to pruneRegulon, addWeights, and calculateActivity

epistasisGA

                   Changes in version 1.11.2                        

• Add reference to maternal/fetal GADGETS paper.
• Update E-GADGETS and Vignette

escape

             Changes in version 2.5.5 (2025-06-11)                  

Bug fix & enhanced functionality

• Enable color.by for both metadata columns and features (other gene sets)
• Introduce summarise.by argument for geyserEnrichment()

• Enable scaling if color.by is another gene.set. Enable scaling for dgCMatrix

             Changes in version 2.5.4 (2025-06-05)                  
  

Bug fixes

• Fix conversion wide-to-long format for heatmapEnrichment()

• Fix issue with t() call on sparse matrices.

             Changes in version 2.5.3 (2025-05-19)                  
  

Highlights

• Streamlined code-base – major internal refactor for clarity, speed and a ~20 % smaller dependency tree.
• Consistent, flexible visualisation API across all plotting helpers.
• Robust unit-test suite (>250 expectations) now ships with the package.

New & enhanced functionality

Performance & dependency reductions

• Replaced plyr, stringr, rlang usage with base-R helpers; these packages are now Suggests only.
• Common color and label utilities (.colorizer(), .colorby(), .orderFunction()) removed redundant tidyverse imports.
• Internal matrices split/chunked with new .split_* helpers to cap memory during parallel scoring/normalization.

Bug fixes

• Gradient mode in ridgeEnrichment() no longer produces grey fills when the chosen gene-set is mapped to color.by.
• pcaEnrichment() axis labels correctly include variance contribution when display.factors = FALSE.
• .grabDimRed() handles both Seurat v5 and <v5 slot structures; fixes missing eigen-values for SCE objects.
• escape.matrix() respects min.size = NULL (no filtering) and handles zero-overlap gene-sets gracefully.
• Global variable declarations consolidated – eliminates R CMD check NOTES regarding na.omit, value, etc.

Documentation

• DESCRIPTION rewritten – heavy packages moved to Suggests; added explicit Config/reticulate for BiocParallel.

• escape.gene.sets data object now fully documented with source, usage, and reference.

             Changes in version 2.4.1 (2025-03-05)                  
  

• Version bump to align with Bioconductor release cycle.
• escape.matrix() now silently removes gene-sets with zero detected features.

EWCE

                   Changes in version 1.17.1                        

• Update maintainer (Alan -> Hiru)
• Fix deprecated ggplot arguments

ExperimentHub

                   Changes in version 2.99.0                        

MAJOR UPDATES

• Update downloading method from httr to httr2

BUG FIXES

• (2.99.1) Add ability to pass config to download resources

• (2.99.2) Add ability to pass progress to download resources

• (2.99.4) Fix call to BiocManager::install. use update=FALSE instead of suppressUpdates=TRUE

• (2.99.6) Update installed.packages to requireNamespace

extraChIPs

                   Changes in version 1.12.1                        

Bug Fixes

• Patched for ggplot2 v4.0.0
• Switched to SimpleUpset for Upset plots

faers

                    Changes in version 1.5.1                        

• Fixed error in handle_setopt(h, …) caused by unsupported option multi_timeout. Requires curl >= 6.0.0.

fenr

                    Changes in version 1.8.2                        

• Stopped using cache in tests, as it might lead to failures in case of a corrupted cache.

fgsea

                   Changes in version 1.35.7                        

• fix handling of zero stat values with gseaParam=0 in plotEnrichment

                   Changes in version 1.35.3                        
  

• plotGesecaTable shows a legend

• plotCoregulationProfileImage for in-situ profiling

• change default color scheme for GESECA plots

• fix GESECA plots for Seurat 5

                   Changes in version 1.35.1                        
  

• more reproducibility between platforms (fix #170), but the exact results differ from previous versions.

FinfoMDS

                   Changes in version 0.99.2                        

• Initial Bioconductor submission.

FLAMES

             Changes in version 2.3.3 (2025-06-18)                  

• Gzipped FASTQ outputs to reduce file size

• Support adding minimap2 indexed genome (as genome_mmi)

• Added crew controllers support, steps can now be submitted to slurm etc.

             Changes in version 2.3.1 (2025-05-22)                  
  

• Refactored pipelines to S4 classes

• Included minimap2, oarfish binaries

• Added a permutation based DTU method in sc_DTU_analysis

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.

FRASER

                    Changes in version 2.4.6                        

• Fixing a bug in the annotation, where we miss the annotation for junction, where we do not have any splice site available at the time of annotation. Thanks to @AtaJadidAhari

                    Changes in version 2.4.5                        
  

• We fixed a bug affecting unstranded paired-end data. We were counting read fragments instead of read pairs. The counted split reads with the fixed method are, on average, lower by around 20%. If you have such data, please rerun your entire analysis from the start (make sure you have recount=TRUE).

                    Changes in version 2.4.4                        
  

• Bugfix: reading fragments instead of read pairs for unstranded paired-end data. If you have such kind of data, please rerun the whole analysis from the start (make sure you have recount=TRUE).

                    Changes in version 2.4.3                        
  

• Fix bug in cache

                    Changes in version 2.4.2                        
  

• Add Optimal Hard Thresholding to determine optimal encoding dimension #69

• Add singular value plot for optimal encoding dimension

• Add updateSeqlevelsStyle to change seqlevels without internet connection

G4SNVHunter

                    Changes in version 1.1.4                        

• Attempting to resolve build issues introduced by the uniquely genius Taishan compilation environment

                    Changes in version 1.1.3                        
  

• Remove .o files

                    Changes in version 1.1.2                        
  

• Tweaked the vignette

                    Changes in version 1.1.1                        
  

• Deprecated functions (still supported but scheduled for removal in a future release):

• checkSNV()

• SNVImpactG4()

  replaced by G4VarImpact()

• filterSNVImpact()

  replaced by filterVarImpact()

• plotSNVImpact()

  replaced by plotVarImpact()

• plotImpactSeq()

  replaced by plotImpactedG4()

• Updated functions:

• G4HunterDetect() | now includes global metadata in the returned object

• Removed functions:

• validateG4HunterParams() | replaced by validateG4HunterDetectInputs()

• New functions:

• exportG4()
• exportMutG4()
• filterVarImpact()
• G4VarImpact()
• loadVariant()
• plotVarImpact()

• plotImpactedG4()

                    Changes in version 1.1.0                        
  

• Bioconductor auto-bumped devel version to 1.1.0 without code changes.

GCPtools

                    Changes in version 1.0.0                        

• Initial Bioconductor release!

gDR

           Changes in version 2025-10-30 (2025-10-30)               

• synchronize Bioconductor and GitHub versioning

           Changes in version 2025-06-11 (2025-06-11)               
  

• update installation instructions

gDRcore

           Changes in version 2025-10-30 (2025-10-30)               

• synchronize Bioconductor and GitHub versioning

           Changes in version 2025-08-12 (2025-08-12)               
  

• fix usage of ifelse

           Changes in version 2025-07-28 (2025-07-28)               
  

• replace row/col_fittings in source for matrix Metrics assay

           Changes in version 2025-07-15 (2025-07-15)               
  

• swap drugs to unify combination order

           Changes in version 2025-07-14 (2025-07-14)               
  

• update headers in fit_SE

           Changes in version 2025-06-10 (2025-06-10)               
  

• switch from lapply into gDRutils::loop in create_SE

           Changes in version 2025-05-22 (2025-05-22)               
  

• add functions for reannotating SummarizedExperiment and MultiAssayExperiment objects

• update vignettes

           Changes in version 2025-05-06 (2025-05-06)               
  

• remove support for masked values

gDRimport

           Changes in version 2025-10-30 (2025-10-30)               

• synchronize Bioconductor and GitHub versioning

           Changes in version 2025-08-12 (2025-08-12)               
  

• fix usage of ifelse

           Changes in version 2025-07-17 (2025-07-17)               
  

• remove run suffix in the PRISM data

           Changes in version 2025-07-10 (2025-07-10)               
  

• add support for new format of private PRISM data

           Changes in version 2025-05-15 (2025-05-15)               
  

• add support for depmap public PRISM data

gDRstyle

           Changes in version 2025-10-30 (2025-10-30)               

• synchronize Bioconductor and GitHub versioning

           Changes in version 2025-08-12 (2025-08-12)               
  

• fix usage of ifelse

           Changes in version 2025-08-04 (2025-08-04)               
  

• added support for skipping vignette building in run_tests.sh

           Changes in version 2025-05-26 (2025-05-26)               
  

• add check for pkgdown in the checkPackage function

gDRutils

           Changes in version 2025-10-30 (2025-10-30)               

• synchronize Bioconductor and GitHub versioning

           Changes in version 2025-09-30 (2025-09-30)               
  

• add predict_smooth_from_combo function

           Changes in version 2025-08-12 (2025-08-12)               
  

• fix usage of ifelse

           Changes in version 2025-08-05 (2025-08-05)               
  

• fix convert_se_assay_to_dt to display appropriate columns

• add flag for capping values in convert_se_assay_to_custom_dt

           Changes in version 2025-08-01 (2025-08-01)               
  

• improve logic in split_SE_components

           Changes in version 2025-07-28 (2025-07-28)               
  

• replace row/col_fittings in source for matrix Metrics assay

           Changes in version 2025-07-14 (2025-07-14)               
  

• add “maxlog10Concentration” and “N_conc” to headers list

           Changes in version 2025-07-01 (2025-07-01)               
  

• refactor average_biological_replicates_dt to properly average data

           Changes in version 2025-06-24 (2025-06-24)               
  

• add support in merge_MAE for merging mixed experiments

           Changes in version 2025-06-09 (2025-06-09)               
  

• update loop to support batch approach

           Changes in version 2025-06-04 (2025-06-04)               
  

• update dependencies

           Changes in version 2025-05-26 (2025-05-26)               
  

• update documentation

           Changes in version 2025-05-21 (2025-05-21)               
  

• add support for combo data in merge_SE

• add merge_MAE fun

           Changes in version 2025-05-13 (2025-05-13)               
  

• add append arg to .set_SE_metadata

           Changes in version 2025-05-12 (2025-05-12)               
  

• improve logic in cap_assay_infinities

           Changes in version 2025-05-07 (2025-05-07)               
  

• update cap_assay_infinities

• add additional grouping columns in cap_assay_infinities

           Changes in version 2025-04-28 (2025-04-28)               
  

• add result entries in headers_list for combination data

           Changes in version 2025-04-17 (2025-04-17)               
  

• refactor get_gDR_session_info to display used packages

gdsfmt

                   Changes in version 1.46.0                        

UTILITIES

• fix a strange bug in append.gdsn(, val=character()) in MacOS when compiled by Apple clang version 17

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

GeneTonic

                    Changes in version 3.4.0                        

Other notes

• The enrichment_map() function now also stores as attribute the original values of the property used to encode the color for the nodes. This change has been made to simplify the transfer of information to any gg-based visual representation where the value-to-color encoding is best left handled in an automated manner (i.e. without enforcing a color-centric attribute, as it is needed within visNetwork)
• The message content returned by the shaker_ functions is not correctly matching the tools they were referring to, thanks @NajlaAbassi for the fix!
• The ggs_backbone() function has been adapted to reflect the latest changes in version >= 3.0.0 of the backbone package. Thanks to @zpneal for the heads up and to @edo98811 for spotting this out (fixes https://github.com/federicomarini/GeneTonic/issues/67)

GenomeInfoDb

                   Changes in version 1.46.0                        

NEW FEATURES

• Started to include a small “chrominfo db” in the package with chromosome info for the most commonly used NCBI and UCSC genome assemblies e.g. GRCh38.p14, GRCh38.p13, GRCm39, hg38, mm39, etc… This makes calls like getChromInfoFromNCBI(“GRCh38.p14”) or getChromInfoFromUCSC(“hg38”) work offline, plus now they are fast and reliable.

SIGNIFICANT USER-VISIBLE CHANGES

• The Seqinfo class was moved from the GenomeInfoDb package to the new Seqinfo package. IMPORTANT WARNING: This means that:
  • Seqinfo-holding S4 objects that were serialized before this change (i.e. prior to Bioconductor 3.22) are no longer valid objects in Bioconductor >= 3.22. However they can be fixed with updateObject().
  • This also means that Seqinfo-holding S4 objects serialized with Bioconductor >= 3.22 are no longer valid objects in Bioconductor < 3.22. These objects can not be fixed with updateObject().

• The GenomeDescription class was also moved from the GenomeInfoDb package to the new Seqinfo package.

• The following functions have moved to the new Seqinfo package:
  • constructor functions Seqinfo() and GenomeDescription()
  • seqinfo(), seqnames(), seqlevels(), seqlevels0()
  • seqlengths()
  • isCircular()
  • genome()
  • orderSeqlevels(), rankSeqlevels()
  • restoreSeqlevels()
  • sortSeqlevels(), seqlevelsInUse()
  • commonName(), provider(), providerVersion()
  • releaseDate(), bsgenomeName()

• The GenomeInfoDb package now depends on new Seqinfo package.

• GenomeInfoDbData was moved from Imports to Suggests (the package is only used by the loadTaxonomyDb() function).

BUG FIXES

• Fix mapping between UCSC genome dm3 and NCBI genome assembly for Drosophila melanogaster Release 5. See commit 3775ca4.

• Fix getChromInfoFromNCBI(“Pan_troglodytes-2.1.4”). See commit 4f3c737.

GenomicAlignments

                   Changes in version 1.46.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• The low-level CIGAR utilities and sequenceLayer() function are now in their own package, the cigarillo package, but with different names. Calling a low-level CIGAR utility function (or sequenceLayer()) defined in GenomicAlignments still works but issues a deprecation warning that indicates the name of the new function to use from cigarillo. For example:

  cigarOpTable(c(“18M4S”, “8M2X5M2I10M”)) M I D N S H P = X [1,] 1 0 0 0 1 0 0 0 0 [2,] 3 1 0 0 0 0 0 0 1 Warning message: In call_new_fun_in_cigarillo(“cigarOpTable”, “tabulate_cigar_ops”, : cigarOpTable() is formally deprecated in GenomicAlignments >= 1.45.5 and replaced with the tabulate_cigar_ops() function from the new cigarillo package

• The package now depends on Seqinfo instead of GenomeInfoDb.

DEPRECATED AND DEFUNCT

• All the low-level CIGAR utilities and the sequenceLayer() function have moved to the new cigarillo package and are now deprecated in GenomicAlignments.

GenomicFeatures

                   Changes in version 1.62.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Drop mirbase.db from Suggests (package got removed from BioC 3.22 after being deprecated in BioC 3.21). As a consequence, function microRNAs() is now defunct.

• The package now depends on the new Seqinfo package instead of GenomeInfoDb.

DEPRECATED AND DEFUNCT

• microRNAs() is defunct.

• All the functions that went to txdbmaker in BioC 3.19 and got formally deprecated in GenomicFeatures in BioC 3.21 are now defunct.

GenomicPlot

                    Changes in version 1.7.2                        

• Add Seqinfo to Imports

• Move GenomeInfoDb from Imports to Suggests

                    Changes in version 1.7.1                        
  

• Updated test function

• Bump up version number to trigger Bioconductor build

                    Changes in version 1.7.0                        
  

• Import seqlevelsStyle from GenomeInfoDb
• Bump up version number

GenomicRanges

                   Changes in version 1.62.0                        

NEW FEATURES

• Add makeGPosFromDataFrame().

SIGNIFICANT USER-VISIBLE CHANGES

• The package depends on Seqinfo instead of GenomeInfoDb.

• The package no longer depends on XVector.

geomeTriD

                   Changes in version 1.13.21                       

IMPROVEMENT

• improve the reset button for tjviewer

                   Changes in version 1.13.20                       
  

IMPROVEMENT

• update the documentations in DESCRIPTION.

                   Changes in version 1.13.19                       
  

IMPROVEMENT

• update the documentations.

• add a reset button for tjviewer

                   Changes in version 1.13.17                       
  

BUG FIXES

• update the author list.

                   Changes in version 1.13.15                       
  

NEW FEATURES

• view3dStructure for multiple sequences.

                   Changes in version 1.13.14                       
  

NEW FEATURES

• Add scale bar in threejsViewer.

                   Changes in version 1.13.13                       
  

BUG FIXES

• Fix the issue for fill_NA if there are multiple NA values in dist matrix.

                   Changes in version 1.13.12                       
  

NEW FEATURES

• Add function to call TADs and compartments for spatial distance.

                   Changes in version 1.13.11                       
  

NEW FEATURES

• Add DSDC distance method for cellDistance.

                   Changes in version 1.13.10                       
  

IMPROVEMENT

• Fix multiple issues for PDF exporter.

                   Changes in version 1.13.9                        
  

NEW FEATURES

• Add NMI and ARI distance method for cellDistance.

                   Changes in version 1.13.8                        
  

IMPROVEMENT

• Add lwd controlor for GenomicInteraction links.

                   Changes in version 1.13.7                        
  

IMPROVEMENT

• Change the default value of normalized for TSS measurement to false.

                   Changes in version 1.13.6                        
  

NEW FEATURES

• Export the function cellDistance.

                   Changes in version 1.13.5                        
  

IMPROVEMENT

• Multiprocess for cellClusters.

                   Changes in version 1.13.4                        
  

NEW FEATURES

• Add function cellClusters.

                   Changes in version 1.13.2                        
  

BUG FIXES

• Move all geos into a sub properties in tjviewer.

                   Changes in version 1.13.1                        
  

NEW FEATURES

• Add hide/show button for each element in tjviewer.

GeomxTools

                   Changes in version 3.12.1                        

• Added pathway information to feature metadata
• Allowed more input types for pheno data (data.frames, lab worksheet) during readNanoStringGeoMxSet
• Bug fix to qcProteinSignal figure axis limit when one or more protein have 0 expression
• Updated tests for Mac and ggplot2 update

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.

gg4way

                    Changes in version 1.6.1                        

• Updates for new major version of ggplot2 and other minor improvements

ggmsa

                   Changes in version 1.15.1                        

• replace ggalt::geom_xspline() with ggfun::geom_xspline() (2017-07-12, Sat)

ggsc

                    Changes in version 1.7.1                        

• compatible with new ggplot2 > 3.5.2 (2025-07-02, Wed)

ggspavis

             Changes in version 1.15.8 (2025-10-05)                 

• add Visium HD and imaging-based visualization to vignette; add sticker

             Changes in version 1.15.6 (2025-05-11)                 
  

• renamed functions plotSpatial() and plotSpatialQC() to plotCoords() and plotObsQC() to avoid function name clash with imcRtools package

             Changes in version 1.15.1 (2025-05-07)                 
  

• support for Visium HD data; renamed functions plotSpots() / plotSpotQC() to plotSpatial() / plotSpatialQC() (contributions by Estella Dong)

ggtree

                   Changes in version 3.99.2                        

• update gheatmap, geom_range and msaplot to compatible with ggplot2 v=4.0.0 (2025-10-16, Thu, #668, #672, #674)
• interactive ggtree (2025-09-16, #662)
• incorporated iggtree, https://github.com/YuLab-SMU/iggtree

• Added support for XStringSet in msaplot (2027-07-13, Sun, #631)

                   Changes in version 3.17.1                        
  

• consistent with ggplot2 v=4.0.0 (2025-07-12, Sat, #657)

ggtreeExtra

                   Changes in version 1.19.1                        

• supporting the ggplot2_v4. (2025-08-08, Fri)

GloScope

             Changes in version 1.99.1 (2025-09-27)                 

• Changed default number of GMM components to 5,10,15,20

             Changes in version 1.99.0 (2025-09-20)                 
  

• Changed name of argument to gloscope and gloscope_proportion from dist_mat to dist_metric to be more consistent in argument names

• Changed name of function gloscope_proportion to gloscopeProp for consistent naming conventions

• gloscopeProp now will calculated the total variation distance between cell-type proportions (dist_metric="TV")

• gloscopeProp now will add the value ep to all counts, not just those that are zero.

• Changed plotMDS to be more versatile. ARGUMENTS HAVE CHANGED. Instead of group_id, user can now give any combination of color_by and shape_by to indicate variables to use for the ggplot. The function has also removed unnecessary ggplot commands, leaving those to the user to chose.

• Added function plotHeatmap as a wrapper to pheatmap function for plotting a heatmap of the GloScope divergence matrix

• Added functions getMetrics, bootstrap_gloscope, bootCI to perform hypothesis testing and confidence intervals for testing differences between groups.

• Added function plotCI to plot output of bootCI

             Changes in version 1.7.2 (2025-09-17)                  
  

• Added functionality for custom GMM and kNN parameters in fitting

• Added aditional test cases and update documentation

             Changes in version 1.7.1 (2025-07-23)                  
  

• Changed default number of GMM components to 6,8,…,24

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

GOexpress

                   Changes in version 1.43.1                        

BUG FIXES

• Remove now unused argument ‘curl’ from all calls to biomaRt::getBM().

GOSemSim

                   Changes in version 2.35.2                        

• bug fixed that introduced in previous commit (2025-10-03, Fri)

• https://github.com/YuLab-SMU/DOSE/issues/86#issuecomment-3361787836

                   Changes in version 2.35.1                        
  

• alternative url for load_onto() (2025-08-12, Tue)

graphite

             Changes in version 1.55.2 (2025-10-22)                 

• Reinstated clipper support.

             Changes in version 1.55.1 (2025-10-22)                 
  

• Automatic cleanup of stale pathway data.

• Updated all pathway data.

GSVA

                    Changes in version 2.40                         

USER VISIBLE CHANGES

• Input needs not row/feature/gene names in the expression data anymore, and gene sets can be directly integer values indexing rows in the expression data. This is mostly useful for quick testing purposes.

• gsvaEnrichment(plot=”ggplot”) outputs now ggplot2 4.0 compliant plots.

• Input (sparse) expression data for the GSVA method can be now also provided as a SVT_SparseMatrix object, defined in the SparseArray package, either directly or within a SingleCellExperiment object. This allows for analysing single-cell data sets with more than 2^31 nonzero values.

• Input expression data for the GSVA method can be now also provided as a DelayedArray matrix storing the values using an HDF5 on-disk backend, either directly or within a SingleCellExperiment object.

• Added a new vignette illustrating the use of the GSVA method with single-cell RNA-seq data.

gVenn

• Initial Submission to Bioconductor

h5mread

                    Changes in version 1.2.0                        

• No changes in this version.

HDF5Array

                   Changes in version 1.38.0                        

• No changes in this version.

hermes

                   Changes in version 1.13.1                        

Bug Fixes

• Fixed issue with draw_boxplot for new ggplot2 version.

HiCPotts

• Initial Submission to Bioconductor

HoloFoodR

                    Changes in version 1.3.1                        

• getMetaboLights: Improve data import.

HPAanalyze

                    Changes in version 1.27                         

• Changes in version 1.27.1
  • Rework hpaDownload for more resilience against changing APIs.
  • Update function documentations
  • Update built-in data and internal gene name lookup table to v24.0
  • Small bug fixes.
• Changes in version 1.27.2
  • Update vignettes
  • Optimize package size
  • Better code comments on download and vis functions

HuBMAPR

                    Changes in version 1.3.2                        

• Error corrections

                    Changes in version 1.3.1                        
  

• Update the functions to display the information properly

Ibex

• Initial Submission to Bioconductor

iCOBRA

                   Changes in version 1.37.1                        

• Minor fixes to tests to be more robust to possible future changes in ggplot2

• Minor rewriting to fix some check notes

imcRtools

             Changes in version 1.15.5 (2025-10-20)                 

• fixed machine imprecision in tests

• fixed test_plotSpatialContext

             Changes in version 1.15.4 (2025-10-08)                 
  

• added readImagefromTIFF function and tests

             Changes in version 1.15.3 (2025-09-26)                 
  

• Added general zscore output to ‘testInteractions()’

• Changed name “histocat” method to “conditional” method in countInteractions and testInteractions

             Changes in version 1.15.2 (2025-06-18)                 
  

• Added “interaction” method to countInteractions and testInteractions

• Added plotInteractions function

                   Changes in version 1.15.1                        
  

• Replaced minDistToCells function with distToCells function

immApex

                    Changes in version 1.3.7                        

UNDERLYING CHANGES

• Ensure buildNetwork() returns a symmetric distance matrix and drops nonstructural zeros

                    Changes in version 1.3.6                        
  

UNDERLYING CHANGES

• Rebuilt propertyEncoder() and onehotEncoder() to use C++ backend with encodeSequences.cpp
• Rebuilt buildNetwork() via C++ integration (fastEditEdges.cpp)
• Motif quantification in calculateMotif() use C++ (calculateMotif.cpp)
• Reduce overall dependencies on external packages
• Improved speed of generateSequences(), mutateSequences(), adjacencyMatrix(), tokenizeSequences(), geometricEncoder
• Added group.by argument to getIR()
• Defunct variationalSequences()
• Removed keras3/tensorflow suggests/dependencies
• Removed baslisk environment, python no longer required
• Updated C++ backend to C++17
• Robust checks before running getIMGT() for website functioning
• Removing special unicode symbols

NEW FEATURES

• calculateEntropy() added to calculate the positional entropy along a biological sequence
• Added basic diversity metrics (exported) to support calculateEntropy()
• calculateFrequency() added to calculate the positional frequency along a biological sequence
• calculateMotif() added to get motif quantification of sequences
• calculateGeneUsage() added for single/paired gene enumeration
• Added scaleMatrix() for comprehensive scale/transformation functions
• Added summaryMatrix() for fast summarization of matrix values

BUGS

• Fixed NT position issue with inferCDR()
• Fixed generateSequence() range issue for single-length sequences
• Fixed binary frequency issue in positionalEncoder()

• Fixed buildNetwork() for relative thresholding returns relative value

                    Changes in version 1.2.2                        
  

• Updated unit tests and vignette check
• Converted package to basilisk from reticulate

immunoClust

                   Changes in version 1.41.1                        

• -CHANGES
  • experimental trail for sub-clustering using kmeans

iModMix

                    Changes in version 1.0.0                        

• Initial Release
  • Introduction of iModMix, a novel network-based approach that integrates multi-omics data, including metabolomics, proteomics, and transcriptomics data.
  • Ability to incorporate both identified and unidentified metabolites.
  • Functions for loading and preprocessing data, performing partial correlation analysis, hierarchical clustering, and module eigengene calculation.
  • Integration of multiple omics datasets to reveal significant associations with phenotypes of interest.
  • Visualization tools for dendrograms, module assignments, and network plots.
  • Enrichment analysis using gene symbols with support for various databases. Key Features
  • load_data(): Function to load and preprocess expression data.
  • partial_cors(): Function to perform partial correlation analysis using Graphical Lasso.
  • hierarchical_cluster(): Function to perform hierarchical clustering using TOM or partial correlation matrix.
  • cluster_assignments(): Function to assign clusters to features based on hierarchical clustering.
  • Eigengenes(): Function to calculate module eigengenes.
  • perform_classification(): Function to relate modules to phenotypes using statistical analysis.
  • Modules_correlation(): Function to integrate multiple omics datasets and calculate correlations.
  • Assigment_genes_enrichr(): Function to perform enrichment analysis using gene symbols.
  • Created documentation and examples for the functions.
  • Added vignette to demonstrate the usage of the package.

IRanges

                   Changes in version 2.44.0                        

NEW FEATURES

• Add makeIRangesFromDataFrame(). Also add:
  • coercion from data.frame or DataFrame to IRanges,
  • support for IRanges(<data.frame>) and IRanges(<DataFrame>).

• Define Views() methods for integer and numeric vectors (they require the XVector package).

• Start experimenting with multithreading in findOverlaps().

SIGNIFICANT USER-VISIBLE CHANGES

• Significantly reduce findOverlaps() memory footprint. See commit 247ed4e.

• Some clarification in nearest()’s documentation.

BUG FIXES

• Small tweak to viewApply() method for Views objects.

ISAnalytics

             Changes in version 1.19.3 (2025-07-21)                 

UPDATE

• colour update for .alluvial_plot

             Changes in version 1.19.2 (2025-07-17)                 
  

UPDATE

• vegan package switched from Suggests to Imports

• added refGene_hg38 for CIS_grubbs test

             Changes in version 1.19.1 (2025-07-09)                 
  

UPDATE

• Changed again color scale for alluvial_plot

             Changes in version 1.19.0 (2025-07-09)                 
  

GENERAL UPDATE

• Changed color scale for alluvial_plot and made some general updates

iscream

• Initial Bioconductor submission

iSEE

                   Changes in version 2.21.1                        

• Fixed dimensions of exported figures.

islify

                    Changes in version 1.1.1                        

• Introduction of the problematicUnevenDistribution flag in the core islify function.

IsoBayes

                    Changes in version 1.6.1                        

• we added a normalization of intensity values (they add to 10,000)

isomiRs

                   Changes in version 1.37.1                        

• Remove functions that were using targetScan since it is not available anymore.

jazzPanda

                    Changes in version 1.1.2                        

Updated on Oct 14, 2025

• Minor bug fix for Bioconductor devel.

                    Changes in version 1.1.1                        
  

Updated on June 24, 2025

Changes to the package include:

• function get_vectors():

• Parameters w_x and w_y have been removed. Spatial windows are now automatically determined per sample using a 5% buffer around the coordinate range.

• Improved handling of genes that are only detected in a subset of samples. If a gene is not present in a sample, a zero-filled vector is used for that sample to maintain consistent vector lengths across samples.

• function create_genesets():

• Parameters w_x and w_y have been removed. Spatial windows are now computed per sample using a 5% buffer based on input coordinates.

• Improved handling of genes that are only detected in a subset of samples. If a gene is not present in a sample, a zero-filled vector is used for that sample to maintain consistent vector lengths across samples.

• function compute_permp():

• Parameters w_x and w_y are no longer required. Spatial boundaries are now automatically derived per sample using a 5% buffer.

                    Changes in version 1.0.1                        
  

Updated on Sep 1, 2025

Changes to the package include:

• function get_vectors():

• Buffer used for auto-detecting spatial windows has been changed from 5% to a fixed value of 1e-6.

• Added a new parameter to allow exporting the calculated bounding box for each sample.

• function compute_permp():

• Buffer for automatic spatial boundaries is now set to 1e-6.

• Fixed spatial bin indexing issues to ensure correct alignment when calcualting spatial vectors with count matrix.

• Backported updates from version 1.1.1 on Bioconductor devel

kebabs

                   Changes in version 1.43.1                        

• updated DESCRIPTION file to new format (Authors@R)

                   Changes in version 1.43.0                        
  

• new branch for Bioconductor 3.22 devel

KEGGREST

                   Changes in version 1.48.1                        

SIGNIFICANT USER-VISIBLE CHANGES

• Defunct mark.pathway.by.objects function (no longer supported).

lefser

                   Changes in version 1.20.0                        

Significant user-visible changes

• Removed blockCol and groupCol arguments in lefser function.

limma

             Changes in version 3.66.0 (2025-10-28)                 

• New argument upshot for treat().

• New argument span for fitFDistUnequalDF1(), squeezeVar() and eBayes().

• The default for adaptive.span in voom() and voomWithQualityWeights() is now TRUE. All the voom functions now use chooseLowessSpan() by default to choose the span.

• New argument xlab for plotSplice() to allow labeling in terms of transcripts or other splicing events instead of exons.

• The help pages for diffSplice(), topSplice() and plotSplice() have been updated to emphasize differential transcript usage instead of differential exon usage or differential splicing. “differential usage” concept tags have been added to the appropriate help pages, creating an entry in the reference manual index.

• makeContrasts() now uses the contrast names if contrasts is a named vector.

• Fix typo in error message from makeContrasts() when the variable names are not syntactically valid.

• Bug fix to contrastAsCoef() when the contrast matrix is not of full column rank.

• The columns of the covariates matrix input to removeBatchEffect() are now mean-corrected.

• removeBatchEffect() now gives a message if design is not specified.

• Bug fix for topTable() when confint=TRUE and either p.value is less than 1 or lfc is greater than zero.

• Revise help page for lmFit(), removing out-of-date mention of default correlation.

• Minor edits to poolVar() and update of help page.

• Complete remaining dates for release versions in NEWS.Rd.

limpa

             Changes in version 1.2.0 (2025-10-28)                  

• New function readFragPipe() to read FragPipe output.

• New function readMaxQuant() to read MaxQuant output.

• readDIANN() now allows user-specified input column names and “parquet” is now the default format.

• Bug fixes to readSpectronaut() when sep is other than a tab or when there is only one peptide annotation column.

• Revisions to all the read functions. readDIANN(), readFragPipe(), readMaxQuant(), and readSpectronaut() all use fread() with data.table=FALSE now to read ascii delimited files.

• New argument logit.p for dztbinom(), which allows the function to avoid subtractive cancellation for success probabilities close to 1. dpc() now uses the new argument when calling dztbinom().

• New function dpcON() to estimate the DPC assuming the oberved-normal model. Should give same output as dpc() but is somewhat faster. dpcON() calls a new function, pztbinomSameSizeLogitPBothTails(), which computes left and right tail p-values for zero-truncated binomial quantiles.

• Revisions to dpcCN() to improve convergence. To improve speed, the function now randomly selects a subset of rows of data to process, with the number of rows given by the new argument subset. The default number of outer iterations is decreased to 2.

• dpcImpute() now sets row.names. Sections on dpcImpute() and imputeByExpTilt() have been added to the package vignette.

• dpcQuant() now calls dpcImpute() automatically when all proteins have just one peptide.

• New function plotPeptides() to plot the peptide-level log-intensities for one protein.

• Fix simProteinDataSet() processing of prop.missing argument.

• Cite the limpa bioRxiv preprint (Li et al, bioRxiv 2025) in the vignette and help pages.

• Expand Quantification section in the vignette to give more math details.

LipidTrend

             Changes in version 0.99.0 (2025-02-25)                 

• Submitted to Bioconductor

LRBaseDbi

                   Changes in version 2.18.1                        

• A vignette modified.

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

Macarron

                   Changes in version 1.13.2                        

• Changed NAs to zeros in calES.R and calQval.R

• Features common across AVA, Qval, and ES are prioritized

                   Changes in version 1.13.1                        
  

• Kept NAs as NAs in calES.R and calQval.R

markeR

• Initial submission to Bioconductor

MassSpecWavelet

             Changes in version 1.75.1 (2025-05-03)                 

• identifyMajorPeaks():

• Properly handle SNR.Th=0 and excludeBoundariesSize=0 cases to bypass those filtering criteria.

• Refactor and include additional peak details such as peakRidgeLengthScale, that can be used to tune ridgeLength; peakNoise, useful to understand the role of w.g. the winSize.noise argument; and selInd, useful to understand which filtering rule is impacting a potential peak from not being identified.

• Fix NOTE on escaping special LaTeX characters

mastR

                    Changes in version 1.9.1                        

• Add Bioinformatics citation for mastR package, add sticker and remove BisqueRNA dependency.

MatrixQCvis

             Changes in version 1.17.1 (2025-06-26)                 

• fix error with respect to setExperimentHubOption in vignette

matter

                   Changes in version 2.11.2                        

NEW FEATURES

• Add ‘as_plotly()’ for coercing vizi plots

                   Changes in version 2.11.1                        
  

BUG FIXES

• Fix S3/S4 method issues with ‘bplapply()’

• Improve to ‘sgmix()’ numeric stability

memes

                   Changes in version 1.17.1                        

• Fixes an error when reading XML files with jagged evalue metadata entries

MetaboAnnotation

                    Changes in version 1.13                         

Changes in 1.13.3

• Expand documentation for CompareSpectraParam to also mention use of msentropy or GNPS-like similarity calculation.

Changes in 1.13.2

• For plotSpectraMirror,MatchedSpectra method, we now pass the available ppm and tolerance value that were used in the creation of the object.

Changes in 1.13.1

• Add parameter matchedPeaksCount to CompareSpectraParam that enables reporting of the number of matched peaks for matchSpectra() with CompareSpectraParam. The result are reported in a column “matched_peaks_count”.

MetaboCoreUtils

                    Changes in version 1.17                         

Changes in 1.17.1

• Fix adductFormula() for negative adducts. and added respective unit test.

MetaboDynamics

                   Changes in version 1.99.12                       

• contains a vignette describing the package workflow with a data frame input
• altered plot_cluster and plot_ORA visualization for patchwork option enabling easier visualization
• all functions require columns names “metabolite”,”condition”,”time” for consistency throughout the package
• get_ORA_annotations() function (retrieving KEGG IDs hierarchies) added back to package
• no more samples in estimates dynamics as probability of clustering solution is implemented now as bootstrapping from model posterior in function cluster_dynamics
• estimates_dynamics() now returns a list with: estimated metabolite abundance (mu), estimated standard deviation of metabolite abundance (sigma), estimated pooled standard deviation per metabolite and dose (lambda), differences in metabolite abundances between time points, euclidean distance between metabolite dynamics of different conditions
• plot_estimates() additionally visualizes the euclidean distance between conditions of metabolite specific dynamics
• cluster_dynamics() provides clustering solution of mean estimates of mu as well as bootstraps clustering solutions
• plot_cluster provides bubbletree, cluster identity, dynamics plots as well as patchwork plot (combining bubbletree, cluster identity and dynamics plots)
• plot_ORA() has now option to be added to bubbletree obtained by plot_cluster
• ORA_hypergeometric() requires now a data frame annotationg metabolites to KEGG IDs (column names “metabolite” and “KEGG”)
• internal adding of ANOVA model with euclidean distance estimation between doses and ANOVA model that integrates cell count uncertainty
• internal adding of simulated cell counts to data(“longitudinalMetabolomics”)

• differences between time points are now ordered and return is a list of plots

                    Changes in version 1.0.2                        
  

Minor bug fix in vignette that caused errors in package checks

                    Changes in version 1.0.1                        

bug fix: fit_dynamics_model() can now correctly handle provided variable names

methylInheritance

                   Changes in version 1.33.1                        

BUG FIXES AND IMPROVEMENTS

• Ensure functions using ggplot2 are using update functions

MetNet

             Changes in version 1.27.4 (2025-10-24)                 

• adjust unit tests for aracne

             Changes in version 1.27.3 (2025-10-23)                 
  

• add 1 as diagonal values in adj in vignette

             Changes in version 1.27.2 (2025-10-10)                 
  

• extend unit test to larger data table in test_methods.R

             Changes in version 1.27.1 (2025-10-02)                 
  

• adjust unit tests after ggplot2 changes

mia

                    Changes in version 1.17                         

• Added add.dimred parameter to meltSE() (2025-04-29)

• Added transformation method that replaces values <= threshold with NA (2025-05-09)

• importMetaPhlAn: Preserve features without taxonomy

• Added agglomerateByModule()

• Added inverse rank normalization (2025-09-10)

miaDash

                    Changes in version 1.1.5                        

• Added Cluster tab

                    Changes in version 1.1.4                        
  

• Switch from csv to tsv support

• Improve interoperability with MGnify datasets

                    Changes in version 1.1.3                        
  

• Introduced tab for Quality Control

                    Changes in version 1.1.2                        
  

• Added importers for HUMAnN, QIIME2 and Mothur

• Improved biom importer

miaTime

• Initial submission to Bioconductor

miaViz

                    Changes in version 1.17                         

• Improve *Histogram and *Barplot by adding options for filling and facetting (2025-04-24)

• Added plotBoxplot function (2025-04-27)

• plotSeries: Improve by adding functionality for sample groups (2025-04-28)

microbiome

             Changes in version 1.32.2 (2025-07-17)                 

• Fixed NEWS file

MicrobiotaProcess

                   Changes in version 1.20.1                        

• rm gghalves since it is not compatible with ggplot2 4.0.0. (2025-09-17, Wed)

MIRit

                    Changes in version 1.5.1                        

The link for downloading miRTarBase v10 has been updated.

miRSM

                    Changes in version 2.5.4                        

• Update s4vd and subspace <2025-06-22, Sun>

                 Changes in version 2.5.1-2.5.3                     
  

• Update linkcomm <2025-06-15, Sun>

miRspongeR

                   Changes in version 2.13.5                        

• Update Groundtruth <2025-10-16, Thur>.

                Changes in version 2.13.1-2.13.4                    
  

• Update linkcomm method <2025-06-15, Sun>.

mitology

                    Changes in version 1.2.0                        

• New enrichMito function to perform a mitochondrial enrichment analysis of a gene list.

• New gseaMito function to perform a mitochondrial GSEA of a gene list.

• New mitoTreePoint function draw a circular dotplot on the mitochondrial gene set tree.

mobileRNA

                    Changes in version 1.5.2                        

• Updated several functions including RNAfeatures.

monaLisa

                   Changes in version 1.15.3                        

• minor updates to adjust to breaking changes in ggplot2 version 4

                   Changes in version 1.15.2                        
  

• minor updates to adjust to functionality migrated from GenomeInfoDb to new Seqinfo package

Moonlight2R

                    Changes in version 1.7.4                        

Summary

• Updated GLS() and GMA() examples to reduce the check timings

                    Changes in version 1.7.3                        
  

Summary

• fixed error in GSEA() module due to issues in DOSE package devel version

                    Changes in version 1.7.2                        
  

Summary

• fixed error in plotDMA and other plotting functions due to updates in tidyHeatmap package

                    Changes in version 1.7.1                        
  

Summary

• fixed error in GLS function due to updates in easyPubMed package

                    Changes in version 1.7.0                        
  

• version bump due to release of Bioconductor 3.21

mosdef

                    Changes in version 1.6.0                        

• Slight edits to have better behaved de_volcano() and go_volcano() functions, with filters/looks depending on the adjusted p-values, and a better management of the color values to be used when plotting the different subsets

MotifPeeker

                    Changes in version 1.1.2                        

Miscellaneous

• Only consider unique peaks in peak count.
• Only return unique peaks in segregate_seqs().

Bug Fixes

• Sanitise peak input names before running FIMO.

                    Changes in version 1.1.1                        
  

Bug Fixes

• Fix importing MACS peak files with no peak names.
• Update tests for messager().

Miscellaneous

• Add citation to pre-print.
• Switch to the official repo for rworkflows.

motifStack

                   Changes in version 1.53.2                        

• Speedup motifHclust

                   Changes in version 1.53.1                        
  

• Support import Hocomoco format.

motifTestR

                    Changes in version 1.5.6                        

• Added GLM-Poisson model for enrichment testing

                    Changes in version 1.5.1                        
  

• Added simMultiMotifs

MPAC

                    Changes in version 1.3.1                        

• updated citation to point to the journal Bioinformatics

msa

                   Changes in version 1.41.3                        

• fix in ClustalOmega to better determine whether OpenMP is available

• updated DESCRIPTION file to new format (Authors@R)

                   Changes in version 1.41.2                        
  

• fix of memory leaks in Muscle (thanks for GitHub user Rong-Zh)

                   Changes in version 1.41.1                        
  

• fix of compilation issues caused by ClustalOmega on arm64 systems

MsBackendMassbank

                    Changes in version 1.17                         

Changes in 1.17.1

• Allow columns/fields “comment” and “data_processing_comment” to have multiple values.

MsBackendMetaboLights

                     Changes in version 1.3                         

Changes in 1.3.2

• Support backendMerge() (issue #10).

Changes in 1.3.1

• Fix download/sync of files with BiocFileCache.

MsBackendSql

                     Changes in version 1.9                         

Changes in 1.9.4

• Add additional unit tests to check results are similar to the reference implementation.

Changes in 1.9.3

• Small performance improvement in longForm() implementation: avoid using findMatches() to order the result if not needed (i.e., if duplicated spectra are requested).

Changes in 1.9.2

• Add a longForm() method for MsBackendSql to use an SQL query to extract the data in long from the database.

Changes in 1.9.1

• Add support for blob2 storage mode for duckdb databases.

MsExperiment

                    Changes in version 1.11                         

Changed in 1.11.1

• Fix readMsExperiment(): if sampleData has row names, they have to match the names of the data files.

MsFeatures

                    Changes in version 1.17                         

MsFeatures 1.17.1

• Add new groupSimilarityMatrixTree() function.

MSnbase

                    Changes in version 2.35                         

2.35.2

• Second fix error from adding Selenocysteine and Pyrrolysine to PSMatch AA table.
• Import PSmatch >= 1.13.3.

2.35.1

• Fix error from adding Selenocysteine and Pyrrolysine to PSMatch AA table.

2.35.0

• New devel version

msqrob2

                    Changes in version 1.17                         

msqrob 1.17.1

• Fixed NEWS file
• Fixed vignette upon renaming of longFormat to longForm

msqrob 1.17.0

• New Bioconductor devel release 3.22

MsQuality

                     Changes in version 1.9                         

Changes in version 1.9.3

• change unit tests for filterEmptySpectra after update

Changes in version 1.9.2

• resolve NAMESPACE issue of unexported objects

Changes in version 1.9.1

• fix bug due to update in rmzqc package, use $new for constructing R6 objects

MSstatsResponse

             Changes in version 1.0.0 (2025-09-22)                  

• Submitted to Bioconductor

MultiAssayExperiment

                   Changes in version 1.36.0                        

New features

• Defunct longFormat generic and methods replaced with longForm
• Added hasRowData method check for assays
• subsetByRowData and intersectByRowData allow filtering of rows based on values in assay rowData (#228)

Bug fixes and minor improvements

• Properly document i subsetByRow and [ bracket methods.
• Match subsetByRow method signatures to generic.

MultiRNAflow

                    Changes in version 1.7.2                        

• Vignette (MultiRNAflow_vignette-knitr.Rnw)

• We use now use.unsrturl=TRUE

                    Changes in version 1.7.1                        
  

• R functions of the packages
• myYlabelNorm() (included in the R function DATAplotExpressionGenes()): there were an error when the RPKM normalization were used.
• GSEAQuickAnalysis():
• replace size aesthetic by linewidth because : Using size aesthetic for lines was deprecated in ggplot2 3.4.0.
• correction errors: print(gManhattan) to print(gproList$gManhattan)
• MFUZZclustersNumber(): slight modification for correcting one warning “Removed 1 row containing missing values or values outside the scale range (geom_point()).”
• DEplotBarplot(): in the section “Examples”, we replace c(“Spe.Pos”, “Spe.Neg”, “Other”) by c(“UpRegulated”, “DownRegulated”, “Other”).
• DEplotBarplotFacetGrid(): in the section “Examples”, we add Melt.Dat.2 <- stats::aggregate(Nb.Spe.DE~., data=Melt.Dat.2, sum) so Melt.Dat.2 is more representative of the data used by our function. We also modify the function to prevent recent warnings from ggplot2 (.data[[“<col_names>“]]).
• Vignette (MultiRNAflow_vignette-knitr.Rnw)
• We add our publication from Bioinformatics
• we correct new errors produced by latex output
• problem with the input max.level of the function str()
• we correct the following new error ‘Illegal parameter number in definition of \NewValue’
• we use ‘\printbibliography’ and ‘\addbibresource’ in the preamble for the ‘cleaner’ biblatex interface.

multistateQTL

             Changes in version 2.1.2 (2025-10-07)                  

• Updated callSignificance so that it works with one state.

             Changes in version 2.1.1 (2025-07-14)                  
  

• Moved data.table to imports instead of depends.
• Updated testing to avoid error with ggplot2 version 4.0.0.

MungeSumstats

                   Changes in version 1.17.5                        

Bug fix

• Before inferring effect column ensure A1 and A2 are uppercase.

                   Changes in version 1.17.3                        
  

Bug fix

• Graciously handle unsinking messages when run fails.

                   Changes in version 1.17.2                        
  

Bug fix

• Bug in long tests utilising ieugwasr - swap to new token system

                   Changes in version 1.17.1                        
  

New features

• MungeSumstats can now handle local versions of dbSNP in tarball format (using the dbSNP_tarball parameter in format_sumstats). This was enabled to help with dbSNP versions >=156, after the decision to no longer provide dbSNP releases as bioconductor packages. dbSNP 156 tarball is available here:http://149.165.171.124/SNPlocs/.

muscat

                   Changes in version 1.23.2                        

• fixed unit test with edge-case failure

• added missing ‘@importFrom grDevices hcl.colors’

• fixed ‘BiocParallel::SerialParam progressbar’ arg

                   Changes in version 1.23.1                        
  

• added bulk-based hypothesis weighing

                   Changes in version 1.23.0                        
  

• Bioconductor 3.21 release

musicatk

             Changes in version 2.2.1 (2025-07-15)                  

• Removed conclust dependency
• Fixed plotting issues with indels
• Cosmetic changes to k value and plotting code

mutscan

• Initial Bioconductor submission

mzR

                   Changes in version 2.43.3                        

• Make electronBeamEnergy an optional header field.

                   Changes in version 2.43.2                        
  

• More fixes around NaN

                   Changes in version 2.43.1                        
  

• Update CV, adds multiple terms

NanoStringNCTools

             Changes in version 1.16.2 (2025-09-26)                 

• Bug fixes for dependency package updates

notame

                     Changes in version 1.0                         

• split notameViz and notameStats from notame

• removed MetaboSet-support

• included SummarizedExperiment-support

• parallelization with BiocParallel

• included website with rworkflows (reference index and vignette also cover notameViz and notameStats)

• removed perform_pairwise_t_test() and perform_paired_t_test(), replaced by perform_t_test()

• removed perform_pairwise_non_parametric() and perform_wilcoxon_signed_rank(), replaced by perform_non_parametric()

• removed align_batches(), replaced by batchCorr::alignBatches()

• removed normalize_batches(), replaced by batchCorr::normalizeBatches()

• other removed functions: install_dependencies(), merge_exprs(), plot_sample_suprahex(), prop_found(), prop_na(), finite helpers such as finite_mean() and simple transformations such as exponential()

• removed plotting in correct_drift(), replaced by save_dc_plots()

• removed plotting in cluster_features(), replaced by visualize_clusters()

• de-exported low-level functionality for drift correction and feature clustering

• renamed read_from_excel() to import_from_excel()

• renamed clean_stats_results() to summarize_results()

• renamed visualizations() to save_QC_plots()

• renamed merge_objects() to merge_notame_sets()

• renamed example_set to toy_notame_set and removed other example data

• reworked vignettes

• reworked plotting functionality in mixOmics_pls() and other mixOmics wrappers

• updated flag_contaminants to use whole number instead of ratio in threshold and include more metrics to flag by

• updated muvr_analysis() to use MUVR2 instead of MUVR package

                   Changes in version 0.99.0                        
  

• submitted to Bioconductor

notameStats

• Initial Bioconductor submission

notameViz

• Initial Bioconductor submission

omicsGMF

• Initial Bioconductor submission

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 4.11.1 (2025-06-09)                 

• Example using WT in interventions.

orthogene

                   Changes in version 1.15.02                       

Bug fixes

• Fix #46

New features

• Disable blank Issues

• Update inst/orthogene manual

                   Changes in version 1.15.01                       
  

Bug fixes

• Update ggplot2 facet calls to avoid deprecation errors.
• Fix all roxygen note warnings.

orthos

                    Changes in version 1.7.3                        

• Update environment definitions

OSTA.data

             Changes in version 1.1.2 (2025-08-28)                  

• add sticker

             Changes in version 1.1.1 (2025-07-21)                  
  

• change Oliveira from biorxiv to Nature Genetics

OUTRIDER

                   Changes in version 1.26.2                        

• Add Optimal Hard Thresholding to determine optimal encoding dimension #69

• Add singular value plot for optimal encoding dimension

• Add highlight.label.size to method-plot.R

peakCombiner

• Initial Bioconductor submission

peakPantheR

             Changes in version 1.23.3 (2025-09-27)                 

• update unittest for ggplot2 4.0.0

• update vignette figures location

Pedixplorer

                    Changes in version 1.5.6                        

• Fix legend plotting when ggplot_gen is TRUE
• Reduce kindepth() warning and error messages to show necessary information.

• Fix lwd usage instead of cex in ped_to_legdf()

                    Changes in version 1.5.5                        
  

• Add label_cex and label_size to control id, date and label text position and size
• Fix csv reading with incoherent number of columns in rows
• Fix check box align_parents in ped_shiny()
• Fix auto_hint() error when couple present twice
• Fix stress computation when individual present more than twice

• Add ind_max_warning and ind_max_error for a better control of pedigree size to plot in shiny application

                    Changes in version 1.5.4                        
  

• Add best_hint computation to the shiny app and split it in different subfunction
• Remove little used library from Imports
• Change shinyWidgets::pickerInput to shiny::selectInput
• Remove 0 from default na_strings
• Update citation to use published article in Bioinformatics
• Add error for _ present in any id columns
• Fix shiny app notification title and slider intermediary value selection
• Fix full scale data reaffection on same column

• Improve position and size of proband label and assymptomatic symbol for logo

                    Changes in version 1.5.3                        
  

• Add short explanation of hints() usage in Pedigree alignment details vignette.

                    Changes in version 1.5.2                        
  

• Fix resizing plot in shiny module by adding dependency

• Update website and readme

                    Changes in version 1.5.1                        
  

• Separate plot management in a shiny module
• Add plot_resize shiny module
• Add help messages using shinyhelper
• Add plink_to_pedigree function to convert plink files to Pedigree object
• Add 0 as one of the default missing identifier value
• Set ggplot generation as independent without plotting on current device
• All draw_* functions return a layer instead of a ggplot object
• Add back message for individuals not plotted
• Add autocompletion of missing twins relationship with complete_twins()

pengls

                   Changes in version 1.15.2                        

• Include citation to publication through CITATION file

                   Changes in version 1.15.1                        
  

• Return named coefficients

pgxRpi

             Changes in version 1.5.3 (2025-05-15)                  

• Added filter_pattern parameter to pgxLoader to enable keyword-based search of available filter terms.
• Improved warning messages to include HTTP status codes for failed requests, and clarified domain information in queries involving multiple domains.
• Simplified domain field description by retaining only the domain address.

PharmacoGx

                   Changes in version 3.13.1                        

• Updated only the sessionInfo fields example data sets due to errors

PhyloProfile

                    Changes in version 2.0.5                        

• auto adjust plot hight for taxonomic labels

• consider 90 percent of input taxa for core gene ident. by default

                    Changes in version 2.0.4                        
  

• show co-orthologs in overview plot

                    Changes in version 2.0.3                        
  

• option to download 3D DIM plot as HTML

                    Changes in version 2.0.2                        
  

• data selection in 3D DIM plot

PMScanR

• Initial Bioconductor submission

PoDCall

             Changes in version 1.17.1 (2025-07-08)                 

• Added alternative way to set threshold in instances when threshold would be returned as NA

podkat

                   Changes in version 1.41.1                        

• updated DESCRIPTION file to new format (Authors@R)

                   Changes in version 1.41.0                        
  

• new branch for Bioconductor 3.22 devel

poem

             Changes in version 1.1.3 (2025-10-21)                  

• Fixed bug of metrics argument not being passed with graph input

                    Changes in version 1.1.2                        
  

• lowMemory argument added to getFuzzyPartitionMetrics()

• returnElementPairAccuracy argument removed from getFuzzyPartitionMetrics(), getFuzzyPartitionGlobalMetrics() and getFuzzyPartitionClassMetrics()

• SpatialAccuracy metric renamed to nsAccuracy for consistency

• Bug fixed in getEmbeddingGlobalMetrics() and getFuzzyPartitionMetrics()

procoil

                   Changes in version 2.37.1                        

• updated DESCRIPTION file to new format (Authors@R)

pRoloc

                    Changes in version 1.49                         

Changes in version 1.49.3

• Bump version for Bioc devel

Changes in version 1.49.2

• Change link to codeberg/lpsvm-tl-code
• An optimised version of tagm_mcmc was implemented. It should be faster and more memory efficient

Changes in version 1.49.1

• Add citation for new f1000 subcellular workflow
• Make defunct setAnnotationParam, getAnnotationParams, showGOEvidenceCodes, getGOEvidenceCodes, addGoAnnotations, orderGoAnnotations and associated helper functions

Changes in version 1.49.0

• New Bioc release

PRONE

                    Changes in version 1.3.2                        

• Now major changes, only applied same changes for Bioconductor release 3.22 version than for version 3.21 -> PRONE 1.2.2

PSMatch

                    Changes in version 1.13                         

PSMatch 1.13.2

• Add CITATION to the pre-print (https://doi.org/10.31219/osf.io/62v9p_v2)
• Add possibility to split protein groups in PSM data with makeAdjacencyMatrix (see issue #30)
• Removed showDetails() from setMethod(“show”, “PSM”) as discussed in issue #30
• Add USI parameter to plotSpectraPTM.
• Correct filterPsmFdr output message
• Update Fragments vignette.
• Improve labelFragments()runtime (see issue #25).
• Add Selenocysteine and Pyrrolysine to getAminoAcids().

PSMatch 1.13.1

• Refactor and improve plotSpectraPTM().

PSMatch 1.13.0

• New Bioconductor devel.

PureCN

                   Changes in version 2.16.0                        

BUGFIXES

• Fixed a crash when GATK log-ratios and a normal coverage file were provided (#386)

• Fixed a few code warnings (e.g. #387)

pwalign

                    Changes in version 1.6.0                        

• No changes in this version.

QFeatures

                    Changes in version 1.19                         

QFeatures 1.19.4

• readQFeatures() doesn’t ignore colData$quantCols (PR #234)
• Create unique precursor ids and use them in joinAssays() (PR #223)
• joinAssays() allows joining based on fcol (PR #247)

QFeatures 1.19.3

• Fixed joinAssays with fcol so that assayLinks are correctly created (PR 247).

QFeatures 1.19.2

• Aggregate features optimisation.

QFeatures 1.19.1

• Fix duplicated fnames bug (see issue #237).
• Use longForm() methods (replacing longFormat(), now defunct).
• Add longForm,SummarizedExperiment, supporting rowvars and colvars, as longForm,QFeatures does. Without this method, uses longForm,ANY that doesn’t.
• Defined a QFeatures object type (bulk or single-cell) in the instance’s metadata slot (developer features).

QFeatures 1.19.0

• New devel version

qpgraph

                    Changes in version 2.44                         

BUG FIXES

• Switch some imports from GenomeInfoDb to the new Seqinfo package.

QTLExperiment

             Changes in version 2.1.3 (2025-10-27)                  

• Changed the data loading function sumstats2qtle(). o Added a flag to skip checking for multiple association tests for combinations of state, feature and variant. o Replaced a left_join with a match which should be faster.

             Changes in version 2.1.2 (2025-09-30)                  
  

• Added support for QTLExperiment objects with only one state, i.e. one column. o sumstats2qtle() can read in data when input has only one path. o mockQTLE() allows nStates = 1.

             Changes in version 2.1.1 (2025-07-14)                  
  

• subset function is now a generic.

RaggedExperiment

                   Changes in version 1.34.0                        

Bug fixes and minor improvements

• Added vignette chunk labels to both vignettes for easier debugging.

RAIDS

                    Changes in version 1.7.3                        

BUG FIXES

o Change default parameters for snpgdsIBDKING() function

Rarr

                     Changes in version 1.9                         

New features

• New functions to work with Zarr attributes have been added:
• read_zarr_attributes() reads Zarr v2 and v3 attributes
• write_zarr_attributes() only supports writing Zarr v2 attributes for now.
• This package now has a pkgdown website, available at https://huber-group-embl.github.io/Rarr/.
• Zarr v3 arrays are now supported for reading metadata via zarr_overview().

Breaking changes

• zarr_overview(as_data_frame = TRUE) now returns information more in line with the output of zarr_overview(as_data_frame = FALSE). In particular:
• a new endianness column has been added to indicate the byte order of the array data.
• the nchunks column is now a list column specifying the number of chunks in each dimension, rather than a single integer giving the total number of chunks.

Minor improvements

• An explicit error message is now given when attempting to read a Zarr array version 3. This version will be supported in a future release of Rarr.

Bug fixes

• .url_parse_other() now accounts for port numbers in host name and colons in S3 buckets.
• writeZarrArray() now allows writing character arrays, and no longer errors complaining about null ‘nchar’ argument value. Default of ‘nchar’ is now NULL.
• writeZarrArray() no longer silently and incorrectly fills the last rows/columns when dim is not divisible by chunk_dim.
• The object name is no longer repeated (e.g., name.zarrname.zarr) when writing a Zarr array to a file in the current working directory.
• Invalid URLs for examples with S3 storage in read_zarr_array() and zarr_overview() have been updated.
• read_zarr_array() no longer errors on arrays with numeric values other than float, int, uint and complex.
• zarr_overview() now returns an explicit error message when the .zarray file is absent

Internal changes

• Coding style throughout the package has been harmonized using the air tool. Contributors using RStudio, Positron or VS Code should have their code styled automatically on save.
• Continuous integration checks have been made stricter by setting biocCheck() error level to “error” rather than “never”, and R CMD check error level to “warning” rather than “error”.
• Static analysis via the lintr package is now performed on each push and PR. It should mostly be invisible to users but might result in slightly increased performance in some cases.
• The superseded httr dependency has been replaced with the lighter curl package, thus reducing the total number of dependencies for the package from 42 to 40.
• The unused stringr dependency has been removed, reducing the total number of dependencies for the package from 40 to 38.
• A minor PROTECT()/UNPROTECT() imbalance in the C code, exposed by rchk, has been fixed. It is not likely to cause problems in real-world situations but it could theoretically lead to crashes in some cases.
• Argument path in internal function read_array_metadata() has been renamed to zarr_path for consistency with other internal functions
• Some internal functions have been renamed with a leading dot, in line with the officially recommended style for Bioconductor packages.
• This package now uses testthat instead of tinytest as a testing framework. This comes with more utilities to handle snapshot tests and mocked tests.
• Function calls are now counted in tests to ensure we don’t repeatedly perform a task (in particular, an expensive I/O task) more often than necessary.

RCM

                   Changes in version 1.25.2                        

• Fixed issues with citation file

                   Changes in version 1.25.1                        
  

• Correct method dispatching for buildConfMat
• Addressing some BiocCheck notes

RCy3

                   Changes in version 2.30.0                        

• fix clearNodePropertyBypass, #229

recount3

                   Changes in version 1.19.3                        

SIGNIFICANT USER-VISIBLE CHANGES

• We have verified that the data hosted by IDIES at JHU is accessible via either https://idies.jhu.edu/recount3/data or https://data.idies.jhu.edu/recount3/data/. See https://github.com/LieberInstitute/recount3/issues/58 for the details.

                   Changes in version 1.19.2                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• recount3 no longer suggests using interactiveDisplayBase::display() as that package will be deprecated on bioc-devel. While the interactive sub-setting of a table was a nice little feature, it was not an important feature. Related to https://github.com/LieberInstitute/recount3/issues/57.

                   Changes in version 1.19.1                        
  

BUG FIXES

• Fixed a bug in file_retrieve() as noted at https://github.com/LieberInstitute/recount3/issues/56. The bug and solution to it was reported by @LiNk-NY.

rhdf5

                   Changes in version 2.54.0                        

CHANGES

• Disabled dataset timestamps, which were applied for compound datasets but not other types. Back ported to 2.52.1. (Thanks to Luke Zappia for reporting this https://github.com/Huber-group-EMBL/rhdf5/issues/160)

• Exposed HDF5 API functions H5Oget_info(), H5Fget_intent() H5Dget_num_chunks().

• Added function h5readTimestamps to extract object timestamp metadata.

• The previously deprecated cset argument in h5createAttribute() has been removed entirely. Please use the encoding argument instead.

rhinotypeR

           Changes in version 2025-10-21 (2025-10-21)               

Fixed

• Example and test errors related to internal helpers (compareAndColorSequences(), compute_cache()) now handled safely using \dontrun{} and updated documentation.
• Removed outdated License stub issue and corrected DESCRIPTION metadata formatting.
• Corrected internal tests referencing deprecated testthat::local_null_device().

Improved

• CountSNPs() re-implementation: directly computes pairwise SNP counts without relying on model-based rounding (e.g., from MSA2dist). No rounding artifacts

           Changes in version 2025-10-01 (2025-10-01)               
  

Added

• New function: alignToRefs(), which aligns user sequences to the packaged rhinovirus prototype references using msa::msa() (ClustalW, ClustalOmega, or MUSCLE), with an option to trim alignments to the non-gap span of a chosen reference.

Improved

• SNPeek() and plotAA(): now support zooming to specific genomic regions and highlighting individual sequences of interest.
• assignTypes(): now reports the genetic distance to the nearest prototype even when the query is “unassigned”.
• Distance calculation: switched to using MSA2dist for pairwise distance computation. This provides broader model support — access to all substitution models in ape::dist.dna, in addition to the “IUPAC” model.
• Data access: prototype and example datasets are now exported as packaged objects (rhinovirusVP4, rhinovirusPrototypesVP4) instead of being accessed via system.file(), simplifying workflows.
• Improved documentation:
• Improved explanations and runnable examples added where feasible.
• Visualization functions return results invisibly to avoid console clutter, while still allowing advanced users to capture outputs.
• Code style and formatting improved (e.g.,consistent internal helpers).

Rhtslib

                    Changes in version 3.6.0                        

• No significant changes in this version.

RNAdecay

                   Changes in version 1.28.1                        

• maintenance - bugs introduced from ggplot2 4.0.0 update fixed.

RnBeads

                   Changes in version 2.27.1                        

• Fixed issue with nv probes. Now they are filtered during the preprocessing.

rrvgo

                   Changes in version 1.21.3                        

• Add new parameter to keep in the output of calculateSimMatrix() terms without Information Content (IC) (reported by GitHub user savagedude3. Thank you!)

• Fixed warning calling calculateSimMatrix() with default value for the semdata parameter (accurately detailed by GitHub user lahuuki. Thank you!)

                   Changes in version 1.21.1                        
  

• Add warning when using children=TRUE in reduceSimMatrix() and no keytype named GOALL in the Orgdb object

rWikiPathways

                   Changes in version 1.29.1                        

• README: cite latest WikiPathways paper

• README: updated a few links (including a relative link)

• README: removed a link to an unmaintained file

• removed .travis.yml

S4Arrays

                   Changes in version 1.10.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Drop dependency on the crayon package.

S4Vectors

                   Changes in version 0.48.0                        

NEW FEATURES

• Add C callable new_SortedByQueryHits_from_IntAEAE.

SIGNIFICANT USER-VISIBLE CHANGES

• Replace C callable new_DataFrame with new_DFrame.

• Convert Rnw slides (rendered as PDF) to Rmd slides (rendered as HTML) (#128). By Marcel Ramos Pérez.

SAIGEgds

                    Changes in version 2.9.2                        

• improve the work load balancing in seqAssocGLMM_SPA() according to SeqArray_1.49.6

• new option ‘verbose.pval’ to improve the display in seqAssocGLMM_SPA()

SanityR

• Initial Bioconductor submission.

scafari

• Initial Bioc submission

scDblFinder

             Changes in version 1.23.1 (2025-07-17)                 

• fixed compatibility issues with xgboost version>=3

scDiagnostics

                    Changes in version 1.4.0                        

• Add functionality to process SCE objects for PCA computation via the new processPCA function.
• Add functionality to downsample SCE objects for diagnostic functions.
• Add new diagnostic functions (calculateTopLoadingGeneShifts, compareMarkers and calculateMMDPValue).
• Add graph integration diagnostic function in replacement of nearest neighbor diagnostic, calculateGraphIntegration.
• Improve regressPC function and plot method, which can now also regress against cell types and batches.
• Improve normalization for plotMarkerExpression diagnostic function.
• Improve user control and options for plot methods.
• Update vignettes to reflect all new changes.

scDotPlot

                    Changes in version 1.2.1                        

• Updates for new major version of ggplot2

scGraphVerse

o Initial Bioconductor Submission

o Project Funding

• Supported by the National Centre for HPC, Big Data and Quantum Computing under the European Union – Next Generation EU – CN00000013 (CUP: B93C22000620006).

scider

             Changes in version 1.8.0 (2025-10-30)                  

• Update help pages
• New function findNbrsGrid() to construct a neighbour list from grid coordinates
• New function findNbrsSNN() to construct a SNN neighbour list from assay
• New function findNbrsSpatial() to construct a distance-based neighbour list from cell coordinates
• New function getNiche() to build a niche assay based on the profile of neighbouring cells
• New function getClusters() to cluster cells in spe using graph methods
• New functions globalMoran() and localMoran() to calculate Moran’s I statistics
• New function normalizeAssay() to perform spatial data normalization
• New function plotDR() for plotting reduced dimensions
• New functions plotImage() and plotLISA() for visualization
• New function realignVisium() to scale and straighten out Visium coordinates
• New functions runPCA() and runUMAP() for performing dimensionality reduction

scLANE

• Initial Bioconductor Submission

scp

                    Changes in version 1.19                         

scp 1.19.5

• Update Seqinfo-holding serialized object(s) to reflect new location of Seqinfo class definition (the class was recently moved from GenomeinfoDb to the new Seqinfo package). Hervé Pagès

scp 1.19.4

• Update scplainer reference.

scp 1.19.3

• docs: explicitly mention scplainer in the man pages

scp 1.19.2

• feat: improved error message when pattern is not found in computeSCR
• feat: use typeMetadata (based on QFeatues 1.19.1)

scp 1.19.1

• fix: moved from the deprecated longFormat() to longForm()
• doc: fixed readSingleCellExperiment example (see #94)
• doc: minor documentation recompilation

scp 1.19.0

• New Bioconductor 3.22 release

scQTLtools

             Changes in version 1.1.4 (2025-05-29)                  

• Updated vignettes and README.

             Changes in version 1.1.3 (2025-05-26)                  
  

• Updated dataset names.
• Updated code comments and documentation.

scrapper

                    Changes in version 1.4.0                        

• Multiple changes to scoreMarkers():

  • Setting all.pairwise= to an integer will now return the top markers by effect size for each pairwise comparison. This is more efficient than creating the 3D array of effects and then ranking the genes in each comparison.

  • The min-rank summary is now limited to the top min.rank.limit= genes, for efficiency. All other genes will have their reported min-rank set to a maximum placeholder.

  • Added compute.group.mean= and compute.group.detected= options to disable reporting of the group-wise means.

• Multiple changes to testEnrichment():

  • Setting universe=NULL will automatically define the universe as the union of all genes.

  • Return value is now a data frame with the number of overlapping genes and the size of each gene set.

• Updated correctMnn() to the new algorithm used by the mnncorrect C++ library. This aims to improve correction accuracy and reduce sensitivity to the choice of reference.

• Bugfix to runAllNeighborSteps() to return an empty list when no step is requested.

• Set bound=0 by default in chooseHighlyVariableGenes(), for more convenient use with residuals.

• Modified scoreGeneSet() to return weights as a data frame containing the row indices of the genes in the set.

• Support character and logical vectors in sets= for aggregateAcrossGenes().

• Automatically remove empty clusters from the output of clusterKmeans().

• Supported blocking and related arguments for weighted averages of distances in scaleByNeighbors().

scRepertoire

                    Changes in version 2.5.7                        

BUG FIXES

• Fixed chain handling for BCR genes in percentGeneUsage() and propagates to wrappers: percentGenes, percentVJ and vizGenes

                    Changes in version 2.5.6                        
  

BUG FIXES

• Fixed passing group.by for combineBCR()

                    Changes in version 2.5.5                        
  

• Update unit tests for ggplot2 v4

                    Changes in version 2.5.3                        
  

BUG FIXES

• Fixed clonalProportion calculation to use grouping properly during combineExpression()

• Fixed immunarch support for exportClones() - TRA/Light chain column handling

                    Changes in version 2.5.2                        
  

• Added support for mouse genes in quietBCRgenes() and quietTCRgenes()

                    Changes in version 2.5.1                        
  

• Introduced pairwise calculations to StartracDiversity()
• Internal function conversion for clonalSizeDistribution() - remove cubature, truncdist and VGAM from dependencies.

• Increased speed of clonalSizeDistribution()

                    Changes in version 2.5.0                        
  

UNDERLYING CHANGES

• Update/Improve code for loadContigs()
• Consolidated support for discrete AIRR formats under the umbrella of AIRR
• Added “tcrpheno” and immunarch to exportClones()
• Converted exportClones() to base R to reduce dependencies
• Added dandelionR vignette to pkgdown site
• Added tcrpheno vignette to pkgdown site
• percentAA() refactored to minimize dependencies and use immApex calculateFrequency()
• positionalEntropy() refactored to minimize dependencies and use immApex calculateEntropy()
• clonalDiversity() refactored for performance - it now calculates a single diversity metric at a time and includes new estimators like “gini”, “d50”, and supports hill numbers).
• percentKmer() refactored to use immApex calculateMotif for both aa and nt sequences. No longer calculates all possible motifs, but only motifs present.
• clonalCluster() now allows for dual-chain clustering, V/J filtering, normalized or straight edit distance calculations, and return of clusters, igraph objects or adjacency matrix
• combineBCR() offers single/dual chain clustering, aa or nt sequences, adaptive filtering of V and J genes and normalized or straight edit distance calculations
• percentGeneUsage() now is the underlying function for percentGenes(), percentVJ(), and vizGenes() and allows for percent, proportion and raw count quantification.
• Added common theme (internal .themeRepertoire()) to all plots and allow users to pass arguments to it

BUG FIXES

• clonalCompare() issue with plotting a 0 row data frame now errors with message
• clonalScatter() group.by/axes call now works for non-single-cell objects
• Fixed issue with NULL and “none” group.by in combineExpression()
• Allowing multi groupings via x.axis and group.by in clonalDiversity()

scRNAseqApp

                   Changes in version 1.9.26                        

• Fix the bug by sanitize the file names when load ATAC track.

                   Changes in version 1.9.25                        
  

• add sum,max to plot type of Sunburst plot panel.

                   Changes in version 1.9.24                        
  

• Add zoom in for plot.

                   Changes in version 1.9.23                        
  

• Fix a bug for file accessibility check.

                   Changes in version 1.9.22                        
  

• Add more color themes

                   Changes in version 1.9.21                        
  

• support for dark mode

                   Changes in version 1.9.20                        
  

• Add support for config.dcf file.

                   Changes in version 1.9.19                        
  

• Add close and delete button for issues.

                   Changes in version 1.9.18                        
  

• Update css for issues.

                   Changes in version 1.9.17                        
  

• Add css for issues.

                   Changes in version 1.9.16                        
  

• Add markdown support for issues.

                   Changes in version 1.9.15                        
  

• Add edit and reply button for issues.

                   Changes in version 1.9.14                        
  

• Fix the test when there is old files in the tmpfolder.

                   Changes in version 1.9.13                        
  

• Handle the file accessibility issue.

                   Changes in version 1.9.12                        
  

• Fix the bug if the script.js does not update.

                   Changes in version 1.9.11                        
  

• Add issues tab.

                   Changes in version 1.9.10                        
  

• Update the homepage to include datasets information.

                    Changes in version 1.9.9                        
  

• Update the unit test.

                    Changes in version 1.9.8                        
  

• Filter cells by a range of value.

                    Changes in version 1.9.7                        
  

• Allow single gene heatmap plot.

                    Changes in version 1.9.6                        
  

• Add progress bar for atac signal plot.

                    Changes in version 1.9.3                        
  

• Adjust the atac peak links plot space.

                    Changes in version 1.9.2                        
  

• Add edge links.

                    Changes in version 1.9.1                        
  

• Fix the issue for ATAC track plot if there is no ‘type’ in peak annotation and no ‘score’ in links.

scTensor

                   Changes in version 2.18.1                        

• A vignette modified.

SeqArray

                   Changes in version 1.50.0                        

NEW FEATURES

• new ‘.status_file’ & ‘.proc_time’ in seqParallel() for controlling the display of the status of child processes

• enhance workload balancing within seqParallel()

• new ‘balancing=NA’ in seqAlleleFreq(), seqAlleleCount(), seqGetAF_AC_Missing(), seqSetFilterCond(), seqUnitFilterCond() (using workload balancing by default)

• new ‘.balancing’ in seqApply() and seqBlockApply()

• new ‘alt’ & ‘ns’ in seqGetAF_AC_Missing()

• new ‘dosage’ in seqExampleFileName()

UTILITIES

• seqDigest() allows a GDS file name in the first argument

• a new option ‘parallel’ in seqDigest()

• seqVCF2GDS() and seqBED2GDS(): save the gds node ‘chromosome’ before ‘position’

• seqAddValue(, varnm="annotation/filter", desp=...) adds ‘Description’ via the argument ‘desp’

• tweak the display of seqGDS2BED()

• seqBlockApply() and seqApply() allows a GDS file name in the first argument

• seqGDS2VCF() generates an indexing file (.tbi) according to the vcf.gz output file, requiring the Rsamtools package

• the first argument of seqOptimize() can be a SeqVarGDSClass object

BUG FIXES

• Previous seqGetAF_AC_Missing(, minor=FALSE) returns the AF for the alt. alleles and the AC for the ref. alleles, when a dosage GDS file is used; a new ‘alt’ is used to specify the ref. or alt. alleles.

• Fix ‘##INFO=<>’ in the output of seqGDS2VCF() when the INFO variable is added by users

Seqinfo

                    Changes in version 1.0.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• The Seqinfo class was moved from the GenomeInfoDb package to the new Seqinfo package. IMPORTANT WARNING: This means that:
  • Seqinfo-holding S4 objects that were serialized before this change (i.e. prior to Bioconductor 3.22) are no longer valid objects in Bioconductor >= 3.22. However they can be fixed with updateObject().
  • This also means that Seqinfo-holding S4 objects serialized with Bioconductor >= 3.22 are no longer valid objects in Bioconductor < 3.22. These objects can not be fixed with updateObject().

SETA

• Initial Bioconductor Release

             Changes in version 0.99.3 (2025-09-15)                 
  

Bioconductor Preparation

• Updated package for Bioconductor review
• Added package-level documentation (?SETA)
• Bioconductor installation instructions
• Added proper error handling for optional dependencies
• Created NEWS file for change tracking

Documentation Improvements

• Added detailed motivation and comparison sections to introductory vignette
• Vignette descriptions with step-by-step explanations
• Added backticks for code formatting throughout vignettes
• Added BiocStyle dependency for proper vignette formatting

Package Structure

• Created R/SETA-package.R with roxygen2 documentation
• Added proper error handling for SeuratObject and SingleCellExperiment dependencies
• Updated DESCRIPTION with BiocStyle dependency

• package-level help with overview

             Changes in version 0.99.1 (2025-08-26)                 
  

New Features

• Initial submission of SETA package for compositional analysis of single-cell RNA-seq data
• Added compositional transform functions (CLR, ALR, ILR, balance)
• Implemented latent space analysis methods (PCA, PCoA, NMDS)
• Created multi-resolution analysis capabilities with hierarchical taxonomies
• Added distance calculation functions for compositional data
• Included vignettes with educational content

Functions Added

• setaCounts(): Extract cell-type count matrices from single-cell objects
• setaTransform(): Apply various compositional transforms
• setaCLR(): Centered log-ratio transformation
• setaALR(): Additive log-ratio transformation
• setaILR(): Isometric log-ratio transformation
• setaBalance(): User-defined balance transformations
• setaPercent(): Percentage transformation
• setaLogCPM(): Log counts-per-million transformation
• setaLatent(): Dimensionality reduction methods
• setaDistances(): Calculate compositional distances
• setaTaxonomyDF(): Create hierarchical taxonomies
• taxonomy_to_tbl_graph(): Convert taxonomies to graph objects
• setaMetadata(): Extract sample-level metadata
• resolveGroup(): Resolve group specifications for balance transforms

Documentation

• Added package documentation
• Created three detailed vignettes:
• Introductory vignette with basic workflow
• Comparing samples vignette with statistical analysis
• Reference frames vignette with multi-resolution analysis
• Added function-level documentation with examples
• Included mathematical foundations and references

Data

• Added mock data functions for testing and examples:
• mockSeurat(): Mock Seurat object
• mockSCE(): Mock SingleCellExperiment object
• mockCount(): Mock count matrix
• mockLong(): Mock long-form data frame

Dependencies

• Core dependencies: dplyr, MASS, Matrix, stats, tidygraph, rlang
• Suggested dependencies: BiocStyle, caret, corrplot, ggplot2, ggraph, knitr, methods, patchwork, reshape2, rmarkdown, SeuratObject, Seurat, SummarizedExperiment, SingleCellExperiment, TabulaMurisSenisData, tidyr, tidytext, testthat

Bioconductor Integration

• Prepared package for Bioconductor submission
• Added BiocStyle dependency for vignette formatting
• Updated README with Bioconductor installation instructions
• Created package-level documentation for ?SETA
• Added NEWS file for change tracking

Testing

• Test suite covering all major functions
• Tests for error handling and edge cases
• Validation of mathematical correctness for transforms
• Mock data testing for integration with single-cell objects

shinybiocloader

                    Changes in version 1.0.0                        

• Initial Bioconductor submission

shinyDSP

                    Changes in version 1.1.2                        

Bug fixes for peer review

• in the setup nav panel, count and annotation tables actually show the first 100 rows.
• added custom BH-adjusted P value input.
• removed ‘turbo’ as an option for heatmap colormap because it’s not a part of hcl.colors(). Instead made all 115 palettes in hcl.colors() available for selection.
• updated the secondary vignette to show RUV4 normalization, differential gene expression analysis, plotting Volcano and heatmaps, and code chunk execution times.

signeR

                   Changes in version 2.11.2                        

• Move VariantAnnotation from Depends to Imports

                   Changes in version 2.11.1                        
  

• Remove survivalAnalysis dependency

• Fixes for some ggplot2 warnings

• Update C++ req to C++14

simPIC

             Changes in version 1.5.3 (2025-04-28)                  

• Extended simPICcountclass object to include: nGroups, batch, differential accessibility, and bcv parameters.
• Updated estimateBCV function in simPICestimate.
• Updates in simPICsimulate:
• simPICsimBatchEffects
• simPICsimBatchCellMeans
• simPICsimulatemultiDA
• simPICsimulateBCVmeans
• simPICsimulateTrueCountsGroups
• Updated vignette to demonstrate new functionality— multiple cell-types

• Removed redundancy in citation in DESCRIPTION

             Changes in version 1.5.2 (2025-04-21)                  
  

• Added package logo to vignette.

             Changes in version 1.5.1 (2025-04-21)                  
  

• Fixing typo in vignette, changed lognormal to lognormal-gamma

SingleCellAlleleExperiment

                    Changes in version 1.5.1                        

Adressing 3.22 devel error for failing test after DropletUtils update Minor changes regarding Links set in documentation

SingleCellSignalR

              Changes in version 2.0 (2024-09-17)                   

• Major Code redesign : Major update based on the use of S4 classes from BulkSignalR.

singleCellTK

             Changes in version 2.18.1 (2025-07-01)                 

• Updated enrichR examples

sketchR

                    Changes in version 1.5.2                        

• Add vignette with workflow examples

SmartPhos

• Initial Bioconductor Submission

            Changes in version 0.99.0 (2025-02-24)                 
  

• SmartPhos package with shinyApp SmartPhos Explorer

• create MultiAssayExperiment object from Spectronaut & MaxQuant files

• different visualization and analysis available.

• possible analysis:

• data transformation and normalization

• data imputation

• batch effect correction

• principal component analyis

• differential expression analyis

• time-series clustering

• geneset enrichment analyis

• phopho-signature enrichment

• kinase activity inference

• visualizations:

• intensity plot

• pca plot

• heatmaps

• volacano plot for differential expression analysis

• p value histogram

• time series plot

• geneset enrichment plots

• kinase activity inference

smoothclust

             Changes in version 1.5.7 (2025-09-15)                  

• optimizations to speed up runtime

smoppix

                    Changes in version 1.1.9                        

• Added citation file to refer to the preprint directly

• Make sure vignettes are build upon installation and mentioned in readme

                    Changes in version 1.1.8                        
  

• Export some convenience functions for other packages

                    Changes in version 1.1.7                        
  

• Remove memory intensive looping over features in data preparation for mixed-effect modelling
• Depend on Rfast package for fast rowsorting

• Include tikzpicture as schematic overview in readme

                    Changes in version 1.1.6                        
  

• Removing functionality related to Moran’s I
• Speed up and reduce memory requirements of linear (mixed) model fitting by preparing design matrices only once

• Correct bug in weighting for cell-wise nn distributions

                    Changes in version 1.1.5                        
  

• Export loadBalanceBplappy for use in other packages

• Mention Bioconductor installer in README

                    Changes in version 1.1.4                        
  

• Optimize addWeightFunction

                    Changes in version 1.1.3                        
  

• Some speedups in the buildDataFrame function

• With reference to bioRxiv preprint

                    Changes in version 1.1.2                        
  

• Calculate nnPair PIs only between desired features

                    Changes in version 1.1.1                        
  

• Allow to pass own colours to plotExplore

SNPRelate

                   Changes in version 1.44.0                        

UTILITIES

• tweak the display (by showing # of variants) when calculating the allele counts and frequencies of a SeqArray GDS file

• tweak the display of date

• import RhpcBLASctl to control the number of threads in BLAS and LAPACK in snpgdsPCA()

• set the threshold ‘missing.rate=0.01’ by default in snpgdsIBDMoM(), snpgdsIBDMLE(), snpgdsIBDKING(), snpgdsDiss(), snpgdsGRM(), snpgdsFst(), snpgdsIndivBeta(), snpgdsIBS(), snpgdsIBSNum(), snpgdsLDpruning(), snpgdsPCA(), snpgdsEIGMIX()

sosta

                    Changes in version 1.1.4                        

• the argument imageCol is now not longer needed in reconstruction functions

• assingCellsToStructures for large datasets and 1 sample

                    Changes in version 1.1.3                        
  

• added sticker and preprint reference

                    Changes in version 1.1.2                        
  

• switch from GenomeInfoDb to new Seqinfo package

                    Changes in version 1.1.1                        
  

• added new function minCellTypeStructDist
• added possibility to reconstruct everything around an object (complement = TRUE)

• relaxed assertion of having at least two cells of each cell type in reconstruction to having at least one of one cell type

                    Changes in version 1.0.1                        
  

• fix problems in when assigning cell to structures

SpaceMarkers

                    Changes in version 2.0.0                        

• Added support for directed cell-cell interaction (see calculate_gene_scores_directed, calculate_influence)
• Functions for supporting ligand-receptor interactions based on directed cell-cell interactions
• Added ligand–receptor and gene-set scoring utilities: calculate_lr_scores, calculate_gene_set_score, and calculate_gene_set_specificity.
• Added support for handling Visium HD
• plotting functions using circlize for showing ligand-receiver interactions.
• API and naming standardization (backwards-incompatible) Major public functions renamed to snake_case for consistency (examples: calcInfluence → calculate_influence, getInteractingGenes → get_interacting_genes, getPairwiseInteractingGenes → get_pairwise_interacting_genes, getSpatialFeatures → get_spatial_features, getSpatialParameters → get_spatial_parameters)

SpaceTrooper

• Initial Bioconductor Submission

spARI

• Submitted to Bioconductor

SparseArray

                   Changes in version 1.10.0                        

NEW FEATURES

• Add the two following capabilities to subassignment of SVT_SparseArray objects:
  • The right value (a.k.a. replacement value) now can be an ordinary array.
  • Using a long linear subscript (i.e. long integer or numeric vector) is now supported. Note that this is also enabled for NaArray objects.

spatialFDA

                   Changes in version 1.1.21                        

• allowing for the explicit passing of correction in spatialInference and crossSpatialInference to fix issues with calculating Lcross.
• passing messages with verbose logical for better usage

• bug fix in tests with removed subsetby argument

                   Changes in version 1.1.20                        
  

• only returning the transformed curves in spatialInference plus removing the assays and the rowData for faster computations.

                   Changes in version 1.1.19                        
  

• fixing plotFbPlot ylims across conditions to have the same range-

                   Changes in version 1.1.18                        
  

• removed the argument subsetby from spatialInference and crossSpatialInference as this will always be the same as image_id in this function

• indicated in the documentation that … in spatialInference and crossSpatialInference is passed to both spatstat.explore functions and to refund::pffr.

                   Changes in version 1.1.17                        
  

• added an assertion that the maximum radius considered must always be smaller than the maximum window length of each image.
• added a test for this case
• add a heuristic to check for a convenient and good rMax to consider

• added heuristic to the vignettes

                   Changes in version 1.1.16                        
  

• adjusted that all failed calcMetricPerFov output NA in the dimension of rSeq, clearly stating which values in metricRes where NA.
• return the raw non-filtered metricResRaw in spatialInference as well as the filtered metricRes for comparison.
• implemented option to add different QC metrics of the functional model and plot them with different shapes in plotCrossHeatmap
• adapted the overview vignette to plot the raw spatial statistics curves

• accelerated all examples and tests with functional GAM via algorithm = “bam”

                   Changes in version 1.1.15                        
  

• added a test to check the edf values and order from the RSE calculation. Made the RSE code more robust.
• added progressbar in crossSpatialInference.

• adapted the overview vignette to reflect the recent changes.

                   Changes in version 1.1.14                        
  

• change the sum of mean residuals per condition to be the residual standard error. The main reason is to have a more comparable estimator of model fit by dividing by the degrees of freedom per condition. The degrees of freedom are the no. of data points per condition (no. of curves * data points per curve)

• the sum of the estimated degrees of freedom of the parameters per condition as provided by the summary.pffr() output.

                   Changes in version 1.1.13                        
  

• provide the condition-wise sum of mean residuals across the curves. This is a measure to judge the quality of the fitted functional GAM by condition.

• allow for an automated threshold selection delta in spatialInference based on the mean over all images of the minimum nearest neighbour distance between points. Added test for this use case

                   Changes in version 1.1.12                        
  

• changed the thresholding in calcMetricPerFov from having at least 1 point per (sub)point pattern to at least two in order to avoid having images with way to uncertain curves. In order to accommodate for this change some tests and examples had to be adapted

• spatialInference now prints the adjusted R squared to quickly assess overall model fit. As this is just one summary, still rigorous assessment via qq plots and autocorrelation should be performed.

                   Changes in version 1.1.11                        
  

• Change in the weighting procedure in spatialInference and no calculation of weights in calcMetricPerFov. It is now possible to define custom weights, by equal weights, by the total number points, and for multitype processes by the smaller point pattern (min) and the larger point pattern (max)
• Option to extract the mean functional coefficient of the functional GAM over the domain $r$ as a measure of the effect size in extractCrossInferenceData

• plotCrossHeatmap creates now a bubble plot with the effect size being the colour and the size of the bubble being the p-value

                   Changes in version 1.1.10                        
  

• p-value adjustment option in plotCrossHeatmap and filtering of coefficients for the heatmap. Fix some small global variable defintion errors

                    Changes in version 1.1.9                        
  

• enabling Fisher’s variance-stabilising transformation in spatialInference as it is recommended for $G$ functions.

                    Changes in version 1.1.8                        
  

• adding a constant to the log in plotCrossHeatmap to avoid NULL values being plotted

                    Changes in version 1.1.7                        
  

• Fixing error in plotCrossHeatmap when the model is NULL.

                    Changes in version 1.1.6                        
  

• Error handling in spatialInference when one condition has no images with curves.

• Wrote as well a new test for this case

                    Changes in version 1.1.5                        
  

• New overview vignette, showing the usability of spatialInference
• Plotting of a heatmap from extracted from crossSpatialInference

• Adding of the package sticker to the README

                    Changes in version 1.1.4                        
  

• functionalGAM accepts flexible naming of the intercept column.

                    Changes in version 1.1.3                        
  

• changed the default of the GAM estimation to be a Gaussian with log link for positivty of the response

                    Changes in version 1.1.2                        
  

• wrote a new convenience function crossSpatialInference which makes the estimation across a range of cell types easier.

                    Changes in version 1.1.1                        
  

• wrote a new convenience function spatialInference which makes the FDA estimation of the spatial statistics functions simpler
• in order to do this various changes to prepData were introduced
• furthermore, small syntactic changes for the retrieval of the functional intercept were added to functionalGam and plotMdl
• The vignette was simplified to reflect the changes in prepData

Spectra

                    Changes in version 1.19                         

Change 1.19.11

• Fix in longForm() method for MsBackendMemory if only peaks variables are extracted.

Change 1.19.10

• Add default implementation of methods for the MsBackend class (issue #338). This reduced code redundancy in Spectra and simplifies implementation of new MsBackend classes considerably.

Change 1.19.9

• Add implementations of spectraVariableMapping() and spectraVariableMapping<- for MsBackend and Spectra objects.

Change 1.19.8

• Add default implementations for MsBackend for replacement methods centroided<-, collisionEnergy<-, dataOrigin<-, isolationWindowLowerMz<-, isolationWindowTargetMz<-, isolationWindowUpperMz<-, msLevel<-, polarity<-, precursorMz<-, rtime<- and smoothed<-. This reduces the amount of methods required to be implemented for new MsBackend classes.

Change 1.19.7

• Add longForm,MsBackend and longForm,Spectra methods (issue #360).

Change 1.19.6

• Add a precursorPurity() function.

Change 1.19.5

• Addition of fragmentGroupIndex() function. This function generates a integer index grouping MSn (MS level > 1) spectra with their corresponding (unique) MS1 spectra based on acquisition order.
• Fix on cbind2() so that the output is a Spectra object and not the backend.

Change 1.19.4

• Fix passing of BPPARAM parameter in peaksData() method for Spectra. Now is being passed down to .peaksapply().

Change in 1.19.3

• Fix in estimatePrecursorMz() that would ignore parameter BPPARAM.

Change in 1.19.2

• Fix export of data using MsBackendMzR: save also the precursor scan number for MSn data (spectra variable “precScanNum”).

Change in 1.19.1

• Add precScanNum() method for MsBackendCached.

SpectraQL

                     Changes in version 1.3                         

Changes in 1.3.1

• Add citation.

SpectriPy

• Initial Submission to Bioconductor

SPICEY

• Initial Submission to Bioconductor

STADyUM

Initial submission to BioConductor.

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

stPipe

• Bioconductor submission.

SummarizedExperiment

                   Changes in version 1.40.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Depends on the new Seqinfo package instead of GenomeInfoDb.

SuperCellCyto

• Initial submission to Bioconductor

SynExtend

                   Changes in version 1.21.2                        

• Deprecated consensus clustering removed from ExoLabel
• ExoLabel now supports argument header=c(FALSE, TRUE, integer(1L)) to skip the first 0,1,n lines of each file (respectively)
• ExoLabel now supports gzip-compressed files as input

• Some examples in man pages have been made faster

                   Changes in version 1.21.1                        
  

• Internal code reorganization for ExoLabel
• Further arguments to SuperTree now correctly passthrough to Treeline

• Some deprecated arguments to EvoWeaver have been removed

                   Changes in version 1.21.0                        
  

• First development version of Bioconductor 3.22

TargetSearch

                   Changes in version 2.12.0                        

NEW FEATURES

• Return intensities and masses as attributes in the output of RIcorrect and RImatrix.

BUG FIXES

• RIcorrect cannot open file under certain conditions. This occurs when the input files are NC4 and the writeCDF4path option is set to write to a different path. Same if they are TargetSearch files, but lack the correct extension.

INTERNAL

• Add new tests for functions RIcorrect and RImatrix.

TaxSEA

             Changes in version 1.1.8 (2025-08-12)                  

• Added output for all taxon sets

• Fixed spelling in GutMGene_producers_of_Phenyalanine

             Changes in version 1.1.7 (2025-08-11)                  
  

• Added Gut-Brain modules database from Valles-Colomer et al. Nature Microbiology. 2019.

             Changes in version 1.1.6 (2025-08-08)                  
  

• Bug fixes

             Changes in version 1.1.5 (2025-08-06)                  
  

• Fixed bug in BacDive Database

             Changes in version 1.1.4 (2025-08-05)                  
  

• Added BacDive Database
• Added Blossum and VANISH taxon sets in disease associations category

TCGAutils

                   Changes in version 1.30.0                        

Significant User-visible changes

• Deprecated mirbase.db package affects mirToRanges function.

Bug fixes and minor improvements

• Use BiocBaseUtils::checkInstalled to check for suggested packages.

TENET

                    Changes in version 1.2.0                        

• Add options to generate violin plots instead of boxplots

• Add support for Jenks natural breaks and custom grouping to step7TopGenesSurvival

• Add support for custom regions and MotifDb filtering options to step7LinkedDNAMethylationSitesMotifSearching

• step7TopGenesUserPeakOverlap now accepts peak names, generates results for each individual peak rather than each peak file, and accepts multiple input objects or directories

• External genomic region files can now be provided as a list of multiple files and/or directories containing them, not just a directory

• Fix TENETSavedSizePlot bug that caused warnings and failure to respect an explicitly specified size

• Fix TENETCacheAllData to fail if any dataset does not exist on the hub

• Significant documentation improvements

• Do not suggest installing the development version of Bioconductor to use the stable version of the package, since it is no longer necessary

• Update installation instructions for Ubuntu 24.04 and add a missing required package

• Add a dependency on ggplot2 4.0 because the example MultiAssayExperiment object now requires it

• Add CITATION file

                    Changes in version 1.1.1                        
  

• Merge survival bug fix from Bioconductor 3.21 release branch; see below

                    Changes in version 1.1.0                        
  

• Release generated automatically by Bioconductor - no changes

TFEA.ChIP

                   Changes in version 1.29.4                        

New Features

• Added a meta-analysis function to combine results across datasets.

• Introduced a new wrapper function that performs the full enrichment workflow in one step, reducing manual intervention.

Enhancements

• Refactored and optimized several core functions for improved performance.

• Improved plotting functions for clearer and more customizable visualizations.

Data Updates

• Updated the ChIPDB object using newly available regulatory region-to-gene annotations from the ENCODE rE2G method and CREdb, enhancing the biological relevance and accuracy of TF-gene associations.

• Integrated new datasets from ReMap.

New default database

• The TF-gene database bundled with TFEA.ChIP was built using the ReMap 2022 ChIP-seq collection and regulatory links from the ENCODE rE2G method. Due to memory constraints, the internal database includes only a subset of the 8,000+ available ChIP-seq experiments. Specifically, we selected 926 experiments performed in the ENCODE Project’s Common Cell Types, prioritizing broadly representative and high-quality datasets.

To download the full database, as well as other ready-to-use databases generated for TFEA.ChIP, visit

• https://github.com/yberda/ChIPDBData

• https://github.com/LauraPS1/TFEA.ChIP_downloads

topdownr

                    Changes in version 1.31                         

Changes in version 1.31.1

• Move package to codeberg.org.

topGO

                   Changes in version 2.62.0                        

• The vignette of topGO is now sporting its new RMarkdown dress, which ideally will make it easier to navigate within the modern browsers
• The documentation of the package is now leveraging the roxygen framework, which should simplify the process of editing it in-sync with the code
• On the sidelines of the whole development process, Federico has been added as a co-maintainer of the package, joining Adrian (the original creator of the package) to possibly propel the creation of additional new features/improvement of the performance

trackViewer

                   Changes in version 1.45.2                        

• Use yaxis to control draw or not for the interaction legend.

• Fix a bug in reading mcool file.

                   Changes in version 1.45.1                        
  

• Fix a bug in reading mcool file.

transmogR

                    Changes in version 1.5.3                        

New Features

• Exported the previously internal function overdispFromBoots() for standalone importing of bootstraps

                    Changes in version 1.5.2                        
  

Bug Fixes

• Switched from ComplexUpset to SimpleUpset as dependency

treeclimbR

                    Changes in version 1.5.1                        

• Add GenomeInfoDb to Suggests

TVTB

             Changes in version 1.35.2 (2025-08-05)                 

Unit test fix

• Fix unit test to match new S7 structure in ggplot2.

txcutr

                   Changes in version 1.15.2                        

NEW FEATURES

• None.

SIGNIFICANT USER-VISIBLE CHANGES

• Removed deprecation notice.
• Updated author email.

BUG FIXES

• Added GenomeInfoDbData to Suggests (Issue #23).

txdbmaker

                    Changes in version 1.6.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Add Seqinfo to Depends and move GenomeInfoDb to Imports.

• Drop mirbase.db from Suggests (package got removed from BioC 3.22 after being deprecated in BioC 3.21). As a consequence, utility function supportedMiRBaseBuildValues() and argument ‘miRBaseBuild’ are now defunct (the latter is an argument of various functions in the package).

DEPRECATED AND DEFUNCT

• Utility function supportedMiRBaseBuildValues() and argument ‘miRBaseBuild’ are defunct (the latter is an argument of various functions in the package).

tximeta

                   Changes in version 1.28.0                        

• Addition of makeLinkedTxpData() a lightweight version of makeLinkedTxome().
• makeLinkedTxome() will now accept a digest and indexName, as an alternative to pointing to a indexDir.
• Addition of three new functions. importData(), inspectDigests(), updateMetadata() allowing import of oarfish (v0.9.0) quantification files when annotated and novel reference transcript sets have been mixed.

• TODO: As of tximeta v1.28.0, some more work is needed to resolve how the add() and retrieve() functions will work, as well as summarizeToGene() for data imported with importData().

                   Changes in version 1.27.11                       
  

• Addition of makeLinkedTxpData() a lightweight version of makeLinkedTxome().

                   Changes in version 1.27.6                        
  

• makeLinkedTxome() will now accept a digest and indexName, as an alternative to pointing to a indexDir.

                   Changes in version 1.27.4                        
  

• Addition of three new functions. importData(), inspectDigests(), updateMetadata() allowing import of oarfish (v0.9.0) quantification files when annotated and novel reference transcript sets have been mixed. TODO: As of tximeta v1.28.0, some more work to do is the development of linkedTxpData and resolving how the add() and retrieve() functions will work, as well as summarizeToGene().

• Major code reorganiziation, splitting out alevin-processing code and moving a number of metadata sub-routines to metadata_helpers.R.

                   Changes in version 1.27.2                        
  

• GENCODE 49 (H.s.), M38 (M.m), and Ensembl 115 (Sep 2025)

                   Changes in version 1.27.1                        
  

• GENCODE 48 (H.s.), M37 (M.m), and Ensembl 114 (May 2025)

UCell

                   Changes in version 2.13.3                        

• New parameter missing_genes to handle missing genes from signatures (either ‘impute’ or ‘skip’)

• New demo to discuss important parameters of the algorithm

• Reformatted scoring function, using gene indices instead of string matches

UCSC.utils

                    Changes in version 1.6.0                        

• No significant changes in this version.

UniProt.ws

                   Changes in version 2.50.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• query input in queryUniProt can now be a named list; clarified in documentation

BUG FIXES AND MINOR IMPROVEMENTS

• collapse in queryUniProt does not need spaces padding, argument is not case-sensitive

universalmotif

                   Changes in version 1.28.0                        

BUG FIXES

• Quiet a couple of warnings triggered during testing the universalmotif initializer function. These warnings should never trigger in real-world scenarios.

updateObject

                   Changes in version 1.14.0                        

• No changes in this version.

UPDhmm

                    Changes in version 1.5.2                        

• Fix vignette for LatEX error.

                    Changes in version 1.5.1                        
  

• Update vignette

                    Changes in version 1.5.0                        
  

• Added parallelization option BPPARAM in calculateEvents() and some new columns in the output.
• Added new vignette: “Preprocessing Guide”.
• Update User Guide vignette
• Add 3 new functions markRecurentRegions(), identifyRecurrentRegions() and collapseEvents()

variancePartition

                    Changes in version 2.0.5                        

• May 31, 2023
• fix convergence issues
• fix initialization of lmer() fit

• use 1 OMP thread internally, then restore to original value

                    Changes in version 2.0.4                        
  

• May 30, 2023
• When running dream(), ensure model convergence using second fitting with Nelder_Mead to avoid edge cases where the approximate hessian from lmerTest::as_lmerModLT() has a negative eigenvalue
• fix issue in get_prediction() returning NA values when variables modeled as categorical and levels are omitted
• fix issue in voomWithDreamWeights() when some genes don’t converge

• retry lmer() model fit with another optimizer after it fails convergence test.

                    Changes in version 2.0.3                        
  

• May 13, 2023

• fix vcov()

                    Changes in version 2.0.2                        
  

• May 17, 2023

• add matrix argument to mvTest()

                    Changes in version 2.0.1                        
  

• May 12, 2023
• mvTest() now shrinks covariance using the Schafer-Strimmer method

• vcovSqrt() returns the matrix whose cross product gives the vcov() result from fits with dream()

                    Changes in version 2.0.0                        
  

• April 20, 2023
• Major code refactoring to:
• improve code reuse
• simplify debugging and maintaining code
• simplify addition of new features
• improve error handling
• some linear mixed model analyses are 50% faster

• enable additional features for dreamlet package that depends heavily on variancePartition.

                   Changes in version 1.39.2                        
  

• update checks to handle voom(…,adaptive.span)

                   Changes in version 1.39.1                        
  

• version bump

velociraptor

                   Changes in version 1.19.1                        

• Switch import of OS-detecting function to basilisk.
• Update scvelo to 0.3.3 (PyPI) for all operating systems.

visiumStitched

                    Changes in version 1.1.1                        

NEW FEATURES

• build_SpatialExperiment() (and add_array_coords()) takes a new parameter algorithm whose default is now “LSAP”. The older implementation is available via the “Euclidean” algorithm. The now LSAP approach is a significant improvement in how new array coordinates are assigned, preventing all duplicate and most empty mappings within a single capture area, leading to improvements in downstream applications like clustering.

xcms

                     Changes in version 4.7                         

Changes in version 4.7.3

• Fix conversion from XcmsExperiment objects to XCMSnExp (issue #807).
• Add parameter columns to chromPeakData() to allow extraction of selected columns.
• Add support for parameter skipFilled to featureSpectra() for XcmsExperiment and XcmsExperimentHdf5 to avoid extraction of spectra for gap-filled chromatographic peaks.
• Fix: add missing import of the spectraData() method from Spectra.
• Add parameter minMzWidthPpm to featureArea() and ChromPeakAreaParam() allowing to define a minima guaranteed m/z width of the feature areas respectively regions to integrate data from for gap-filling (issue #756).

Changes in version 4.7.2

• Change default for [,XcmsExperiment and [,XcmsExperimentHdf5 keepAdjustedRtime from FALSE to TRUE.
• Fix issue in [,XcmsExperiment: the subset operation did not revert the retention times of chromatographic peaks with parameter keepAdjustedRtime = FALSE (issue #801).
• Fix issue in chromPeakSpectra for XcmsExperiment with duplicated chrom peak IDs (issue #796).
• Fix issue in chromPeakSpectra() for XcmsExperiment that added column (sample) names to the resulting XChromatograms object with newer versions of the MsExperiment package (>= 1.11.1); issue #803.

Changes in version 4.7.1

• Change the naming convention of chromatographic peaks to include also the MS level after “CP”: “CP1001” instead of “CP001” for a chromatographic peak in MS level 1 or “CP2001” instead of “CP001” for a chromatographic peak in MS level 2.
• Massively reduce main memory demand of xcms with the new on-disk storage mode of the preprocessing results: the new XcmsExperimentHdf5 result object stores all preprocessing results in an HDF5 file.
• Optimization and performance improvements for extraction of chromatographic data. This includes using MsCoreUtils::reduce().
• Restructure and clean-up of documentation.
• Don’t export unnecessary get/set methods for Param classes.
• Throw an error if parameters mz or rt for chromatogram() contain missing values.

zellkonverter

                   Changes in version 1.20.0                        

New features

• Add an environment for anndata v0.12.3. This is now the default.

• Add a message recommending the anndataR package

Major changes

• Update Python environments for compatibility with the new basilisk system

Minor changes

• Adapt to changes in DelayedArray v0.35.2

NEWS from existing Data Experiment Packages

ChIPDBData

• first version of the package

curatedMetagenomicData

                   Changes in version 3.16.1                        

• Updates to rownames = “short” due to downstream changes in mia (@TuomasBorman, #309)

• Use convertToPhyloseq in vignette instead of makePhyloseqFromTreeSummarizedExperiment (@cmirzayi, #310)

• Use rep_named instead of deprecated list_along (@LiNk-NY)

curatedTCGAData

                   Changes in version 1.32.0                        

Bug fixes and minor improvements

• Added chunk labels to vignette

• Improvements to GitHub Actions workflows

DoReMiTra

• Initial Bioconductor submission

iModMixData

                   Changes in version 0.99.0                        

Initial Release

mCSEAdata

                   Changes in version 1.29.1                        

• Added support for EPICv2 platform.

MetaScope

                    Changes in version 3.23                         

Bug fixes

• fixed the metascope_id() function to export the location of the id file

• Made significant improvements in memory usage in Metascope_id

                    Changes in version 3.22                         
  

Bug Fixes

• Fixed filter compression to take a pre-formatted character string in csv format

• Fixed minor issues in convert_animalcules() when non-linked taxonomy IDs are present

• Updated convert_animalcules to correct a bug in the final consolidation of reads, where more read counts were being added than in the original sample

nmrdata

• Initial submission to Bioconductor.

• Provides curated 1D ^1H NMR spectra of rat (murine) urine samples from a bariatric surgery study.

• Includes two datasets:

• Processed dataset (bariatric) accessible via loadBariatric().

• Raw Bruker NMR experiment folders accessible via getRawExpDir().

RforProteomics

                   Changes in version 1.47.2                        

• Use latest MSnbase

                   Changes in version 1.47.1                        
  

• Remove DEP suggests.

• Update vignettes: remove some references to old/outdated packages, add note about RforMS.

SingleCellMultiModal

                   Changes in version 1.22.0                        

Bug fixes and minor improvements

• Updated vignette authorship information

• Added sticker to README.md

• Enhancements to GitHub Actions workflows

spatialLIBD

                   Changes in version 1.21.6                        

NEW FEATURES

• registration_pseudobulk() will now create the rowData()$gene_search if rowData()$gene_id and rowData()$gene_name are present. This makes the output be more in sync with requirements for run_app(). See https://github.com/LieberInstitute/spatialLIBD/pull/115 for details. Implemented by @lahuuki.

                   Changes in version 1.21.4                        
  

BUG FIXES

• @manishabarse fixed a bug in registration_wrapper() which led to NULL results for anova. See https://github.com/LieberInstitute/spatialLIBD/pull/110 for details.

                   Changes in version 1.21.3                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• @lahuuki edited registration_pseudobulk() to make it more compatible with scran::pseudobulkDGE().See https://github.com/LieberInstitute/spatialLIBD/pull/108 for details.

                   Changes in version 1.21.2                        
  

NEW FEATURES

• @lahuuki added the vis_image() for plotting just the histology image. See https://github.com/LieberInstitute/spatialLIBD/pull/107 for details.

                   Changes in version 1.21.1                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• The documentation of registration_pseudobulk() has been expanded to further explain the logcounts() assay. That is, to highlight that this assay contains log2 CPM values computed with edgeR::cpm() and not log2 library-size normalized counts (as computed with scuttle::logNormCounts()). See https://support.bioconductor.org/p/9161754 and https://github.com/LieberInstitute/spatialLIBD/issues/106 by @kinnaryshah for more details.

STexampleData

             Changes in version 1.17.1 (2025-10-05)                 

• add sticker

TENET.ExperimentHub

                    Changes in version 1.1.2                        

• Correct Location_Prefix as per Bioconductor staff email

                    Changes in version 1.1.1                        
  

• Regenerate the example MultiAssayExperiment object with ggplot2 4.0, because it cannot load objects saved by previous ggplot2 versions. Since the reverse is also true, add a dependency on ggplot2 4.0.

• Correct the name of a dataset loaded from TENET in make-data.R, which was changed late in the development process but not changed in this script

• Update the link to the example TAD dataset to use the Internet Archive since the original URL is no longer accessible

• Do not suggest installing the development version of Bioconductor to use the stable version of the package, since it is no longer necessary

• Update installation instructions for Ubuntu 24.04 and add a missing required package

• Add CITATION file

• Add TENET to Suggests field in DESCRIPTION

                    Changes in version 1.1.0                        
  

• Release generated automatically by Bioconductor - no changes

Deprecated and Defunct Packages

SOFTWARE:

Thirty nine software packages were removed from this release (after being deprecated in Bioc 3.21):

• 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

Forty software packages are deprecated in this release and will be removed in Bioc 3.23:

• bgx, BiGGR, biodbHmdb, biodbNcbi, biodbNci, biodbUniprot, ccmap, CellScore, CINdex, cisPath, DEP, gpuMagic, Harshlight, hiAnnotator, hiReadsProcessor, hypeR, interactiveDisplay, interactiveDisplayBase, lapmix, LinTInd, lute, MADSEQ, netZooR, oppti, PhenStat, qckitfastq, ReactomeGraph4R, Repitools, Rfastp, rGADEM, rRDP, SARC, seqArchR, seqArchRplus, seqTools, Streamer, TitanCNA, TransView, traviz, XNAString

EXPERIMENT DATA:

Three experimental data packages were removed from this release (after being deprecated in BioC 3.21):

• benchmarkfdrData2019, parathyroidSE, synapterdata

Five experimental data packages are deprecated in this release and will be removed in Bioc 3.23:

• AneuFinderData, chromstaRData, curatedCRCData, RGMQLlib, rRDPData

ANNOTATION DATA:

Three annotation packages were removed from this release (after being deprecated in Bioc 3.22).

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

No annotation packages are deprecated in this release.

WORKFLOWS:

One workflow packages was removed from this release (after being deprecated in Bioc 3.22).

• BiocMetaWorkflow

One workflow package is deprecated in this release and will be removed in Bioc 3.23:

• spicyWorkflow

BOOKS:

No books were removed from this release.

No books were deprecated in this release.