bioc-release.r-universe.dev

[bioc-release] igblastr 1.2.9

hpages.on.github@gmail.com (Hervé Pagès) — Wed, 10 Jun 2026 07:24:52 GMT

The igblastr package provides functions to conveniently install and use a local IgBLAST installation from within R. The package also includes a set of built-in IgBLAST-compatible germline databases from OGRDB, the AIRR Community’s Open Germline Receptor Database, for various organisms. It provides functions to create additional IgBLAST-compatible germline databases using reference sequences retrieved from IMGT/V-QUEST or local FASTA files supplied by the user. When possible, annotations for the V and J alleles in a new germline database are automatically computed and added to the database, so they can be used as replacements for the internal and auxiliary data provided by IgBLAST. IgBLAST is described at . IgBLAST web interface: . OGRDB: . IMGT/V-QUEST download site: .

[bioc-release] rfaRm 1.24.1

rafael.ayala@oist.jp (Lara Selles Vidal) — Wed, 10 Jun 2026 01:05:27 GMT

rfaRm provides a client interface to the Rfam database of RNA families. Data that can be retrieved include RNA families, secondary structure images, covariance models, sequences within each family, alignments leading to the identification of a family and secondary structures in the dot-bracket format.

[bioc-release] Rega 1.0.2

igor.cervenka@unibas.ch (Igor Cervenka) — Tue, 09 Jun 2026 14:09:03 GMT

The European Genome-phenome Archive (EGA) provides long-term storage and controlled sharing of personally identifiable genetic data. The Rega package offers a streamlined and extensible R interface to the EGA API, facilitating the programmatic upload of metadata. GEO-like Excel submission template is provided as a default method of organizing submission metadata.

[bioc-release] SPONGE 1.34.1

markus.list@tum.de (Markus List) — Tue, 09 Jun 2026 09:07:51 GMT

This package provides methods to efficiently detect competitive endogeneous RNA interactions between two genes. Such interactions are mediated by one or several miRNAs such that both gene and miRNA expression data for a larger number of samples is needed as input. The SPONGE package now also includes spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape.

[bioc-release] Spectra 1.22.2

maintainer@rformassspectrometry.org (RforMassSpectrometry Package Maintainer) — Mon, 08 Jun 2026 13:37:21 GMT

The Spectra package defines an efficient infrastructure for storing and handling mass spectrometry spectra and functionality to subset, process, visualize and compare spectra data. It provides different implementations (backends) to store mass spectrometry data. These comprise backends tuned for fast data access and processing and backends for very large data sets ensuring a small memory footprint.

[bioc-release] BgeeCall 1.28.2

julien.wollbrett@unil.ch (Julien Wollbrett) — Mon, 08 Jun 2026 10:28:07 GMT

BgeeCall allows to generate present/absent gene expression calls without using an arbitrary cutoff like TPM<1. Calls are generated based on reference intergenic sequences. These sequences are generated based on expression of all RNA-Seq libraries of each species integrated in Bgee (https://bgee.org).

[bioc-release] profileplyr 1.28.3

doug.barrows@gmail.com (Doug Barrows) — Thu, 04 Jun 2026 17:51:18 GMT

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

[bioc-release] ggtreeExtra 1.22.1

xshuangbin@163.com (Shuangbin Xu) — Thu, 04 Jun 2026 06:23:33 GMT

'ggtreeExtra' extends the method for mapping and visualizing associated data on phylogenetic tree using 'ggtree'. These associated data can be presented on the external panels to circular layout, fan layout, or other rectangular layout tree built by 'ggtree' with the grammar of 'ggplot2'.

[bioc-release] rhdf5client 1.34.2

alsergbox@gmail.com (Alexey Sergushichev) — Mon, 01 Jun 2026 18:46:19 GMT

This package provides functionality for reading data from HDF Scalable Data Service from within R. The HSDSArray function bridges from HSDS to the user via the DelayedArray interface. Bioconductor manages an open HSDS instance graciously provided by John Readey of the HDF Group.

[bioc-release] scDblFinder 1.26.2

pierre-luc.germain@hest.ethz.ch (Pierre-Luc Germain) — Mon, 01 Jun 2026 18:33:18 GMT

The scDblFinder package gathers various methods for the detection and handling of doublets/multiplets in single-cell sequencing data (i.e. multiple cells captured within the same droplet or reaction volume). It includes methods formerly found in the scran package, the new fast and comprehensive scDblFinder method, and a reimplementation of the Amulet detection method for single-cell ATAC-seq.

[bioc-release] PhyloProfile 2.4.1

tran@bio.uni-frankfurt.de (Vinh Tran) — Mon, 01 Jun 2026 10:02:57 GMT

PhyloProfile is a tool for exploring complex phylogenetic profiles. Phylogenetic profiles, presence/absence patterns of genes over a set of species, are commonly used to trace the functional and evolutionary history of genes across species and time. With PhyloProfile we can enrich regular phylogenetic profiles with further data like sequence/structure similarity, to make phylogenetic profiling more meaningful. Besides the interactive visualisation powered by R-Shiny, the package offers a set of further analysis features to gain insights like the gene age estimation or core gene identification.

[bioc-release] limma 3.68.4

smyth@wehi.edu.au (Gordon Smyth) — Sun, 31 May 2026 08:19:44 GMT

Data analysis, linear models and differential expression for omics data.

[bioc-release] psichomics 1.38.1

nunodanielagostinho@gmail.com (Nuno Saraiva-Agostinho) — Sat, 30 May 2026 22:21:18 GMT

Interactive R package with an intuitive Shiny-based graphical interface for alternative splicing quantification and integrative analyses of alternative splicing and gene expression based on The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression project (GTEx), Sequence Read Archive (SRA) and user-provided data. The tool interactively performs survival, dimensionality reduction and median- and variance-based differential splicing and gene expression analyses that benefit from the incorporation of clinical and molecular sample-associated features (such as tumour stage or survival). Interactive visual access to genomic mapping and functional annotation of selected alternative splicing events is also included.

[bioc-release] SeqArray 1.52.1

zhengx@u.washington.edu (Xiuwen Zheng) — Sat, 30 May 2026 05:02:14 GMT

Data management of large-scale whole-genome sequencing variant calls with thousands of individuals: genotypic data (e.g., SNVs, indels and structural variation calls) and annotations in SeqArray GDS files are stored in an array-oriented and compressed manner, with efficient data access using the R programming language.

[bioc-release] Rarr 2.0.1

hugo.gruson@embl.de (Hugo Gruson) — Fri, 29 May 2026 09:25:29 GMT

The Zarr specification defines a format for chunked, compressed, N-dimensional arrays. It's design allows efficient access to subsets of the stored array, and supports both local and cloud storage systems. Rarr aims to implement this specification in R with minimal reliance on an external tools or libraries.

[bioc-release] BiocBaseUtils 1.14.2

marcel.ramos@sph.cuny.edu (Marcel Ramos) — Tue, 26 May 2026 21:25:06 GMT

The package coalesces typical helper functions that are scattered throughout the Bioconductor ecosystem. It aims to reduce code redundancy by formalizing functions often used by Bioconductor developers. These functions include operations such as replacing slots in an object, selecting observations for show methods, labeling function life cycles, and more.

[bioc-release] AnVILGCP 1.6.2

marcel.ramos@sph.cuny.edu (Marcel Ramos) — Tue, 26 May 2026 21:04:29 GMT

The package provides a set of functions to interact with the Google Cloud Platform (GCP) services on the AnVIL platform. The package is designed to use the API calls from the AnVIL package. It coordinates AnVIL workspace functionality with native GCP tools.

[bioc-release] GCPtools 1.2.1

marcel.ramos@sph.cuny.edu (Marcel Ramos) — Tue, 26 May 2026 20:50:15 GMT

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.

[bioc-release] DelayedArray 0.38.2

hpages.on.github@gmail.com (Hervé Pagès) — Tue, 26 May 2026 17:05:47 GMT

Wrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, ordinary arrays and, data frames.

[bioc-release] pipeComp 1.22.1

pierre-luc.germain@hest.ethz.ch (Pierre-Luc Germain) — Tue, 26 May 2026 07:26:25 GMT

A simple framework to facilitate the comparison of pipelines involving various steps and parameters. The `pipelineDefinition` class represents pipelines as, minimally, a set of functions consecutively executed on the output of the previous one, and optionally accompanied by step-wise evaluation and aggregation functions. Given such an object, a set of alternative parameters/methods, and benchmark datasets, the `runPipeline` function then proceeds through all combinations arguments, avoiding recomputing the same step twice and compiling evaluations on the fly to avoid storing potentially large intermediate data.

[bioc-release] CellMentor 1.0.1

petrenko.kate@icloud.com (Ekaterina Petrenko) — Mon, 25 May 2026 16:23:09 GMT

Implements supervised cell type-aware non-negative matrix factorization (NMF) for dimensional reduction in single-cell RNA sequencing analysis. The package provides methods for incorporating cell type information into the dimensionality reduction process, enabling improved visualization and downstream analysis of single-cell data while preserving biological structure. CellMentor employs a unique loss function that simultaneously minimizes variation within known cell populations while maximizing distinctions between different cell types, enabling effective transfer of learned patterns from labeled reference datasets to new unlabeled data.

[bioc-release] ensembldb 2.36.1

johannes.rainer@eurac.edu (Johannes Rainer) — Mon, 25 May 2026 09:23:58 GMT

The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, ensembldb provides a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes. EnsDb databases built with ensembldb contain also protein annotations and mappings between proteins and their encoding transcripts. Finally, ensembldb provides functions to map between genomic, transcript and protein coordinates.

[bioc-release] assorthead 1.6.3

infinite.monkeys.with.keyboards@gmail.com (Aaron Lun) — Mon, 25 May 2026 07:11:23 GMT

Vendors an assortment of useful header-only C++ libraries. Bioconductor packages can use these libraries in their own C++ code by LinkingTo this package without introducing any additional dependencies. The use of a central repository avoids duplicate vendoring of libraries across multiple R packages, and enables better coordination of version updates across cohorts of interdependent C++ libraries.

[bioc-release] scMitoMut 1.8.0

sunwjie@gmail.com (Wenjie Sun) — Mon, 25 May 2026 05:23:52 GMT

This package is designed for calling lineage-informative mitochondrial mutations using single-cell sequencing data, such as scRNASeq and scATACSeq (preferably the latter due to RNA editing issues). It includes functions for mutation calling and visualization. Mutation calling is done using beta-binomial distribution.

[bioc-release] TCGAutils 1.32.1

marcel.ramos@sph.cuny.edu (Marcel Ramos) — Mon, 25 May 2026 02:25:40 GMT

A suite of helper functions for checking and manipulating TCGA data including data obtained from the curatedTCGAData experiment package. These functions aim to simplify and make working with TCGA data more manageable. Exported functions include those that import data from flat files into Bioconductor objects, convert row annotations, and identifier translation via the GDC API.

[bioc-release] edgeR 4.10.1

mark.robinson@imls.uzh.ch (Yunshun Chen) — Sat, 23 May 2026 03:30:36 GMT

Differential expression analysis of sequence count data. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models, quasi-likelihood, and gene set enrichment. Can perform differential analyses of any type of omics data that produces read counts, including RNA-seq, ChIP-seq, ATAC-seq, Bisulfite-seq, SAGE, CAGE, metabolomics, or proteomics spectral counts. RNA-seq analyses can be conducted at the gene or isoform level, and tests can be conducted for differential exon or transcript usage.

[bioc-release] GraphExperiment 1.0.1

fabricio_almeidasilva@hotmail.com (Fabricio Almeida-Silva) — Fri, 22 May 2026 19:37:38 GMT

GraphExperiment provides users and developers with an S4 class that extends `SingleCellExperiment` by offering infrastructure to store and retrieve networks (`igraph` objects) representing how assay features and/or observations are associated with each other. The class was designed to store networks inferred from high-dimensional quantitative data, with feature-feature networks including gene coexpression networks (GCNs), gene regulatory networks (GRNs), and co-abundance networks (from proteomics and metabolomics), and observation-observation network including cell-cell distances, species-species relationships, and sample-sample similarities.

[bioc-release] MsBackendMetaboLights 1.6.1

johannes.rainer@eurac.edu (Johannes Rainer) — Fri, 22 May 2026 12:31:40 GMT

MetaboLights is one of the main public repositories for storage of metabolomics experiments, which includes analysis results as well as raw data. The MsBackendMetaboLights package provides functionality to retrieve and represent mass spectrometry (MS) data from MetaboLights. Data files are downloaded and cached locally avoiding repetitive downloads. MS data from metabolomics experiments can thus be directly and seamlessly integrated into R-based analysis workflows with the Spectra and MsBackendMetaboLights package.

[bioc-release] Biostrings 2.80.1

hpages.on.github@gmail.com (Hervé Pagès) — Fri, 22 May 2026 06:02:45 GMT

Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.

[bioc-release] dmGsea 1.2.1

xuz@niehs.nih.gov (Zongli Xu) — Thu, 21 May 2026 16:58:57 GMT

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.

[bioc-release] normr 1.38.1

johannes.helmuth@laborberlin.com (Johannes Helmuth) — Thu, 21 May 2026 16:33:14 GMT

Robust normalization and difference calling procedures for ChIP-seq and alike data. Read counts are modeled jointly as a binomial mixture model with a user-specified number of components. A fitted background estimate accounts for the effect of enrichment in certain regions and, therefore, represents an appropriate null hypothesis. This robust background is used to identify significantly enriched or depleted regions.

[bioc-release] bamsignals 1.44.1

johannes.helmuth@laborberlin.com (Johannes Helmuth) — Thu, 21 May 2026 15:32:16 GMT

This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired-end data.

[bioc-release] MicrobiomeProfiler 1.18.1

guangchuangyu@gmail.com (Guangchuang Yu) — Thu, 21 May 2026 01:10:29 GMT

This is an R/shiny package to perform functional enrichment analysis for microbiome data. This package was based on clusterProfiler. Moreover, MicrobiomeProfiler support KEGG enrichment analysis, COG enrichment analysis, Microbe-Disease association enrichment analysis, Metabo-Pathway analysis.

[bioc-release] BiocBuildReporter 1.0.1

lori.shepherd@roswellpark.org (Lori Shepherd) — Wed, 20 May 2026 15:02:30 GMT

This package reads remote parquet files that have processed Bioconductor build report logs. Users may query the tables directly for specific information or use pre-defined helper functions for common queries. The logs processed are from https://bioconductor.org/checkResults/. In the future we will extend this package out to include processing of r-universe logs.

[bioc-release] scater 1.40.1

alan.ocallaghan@outlook.com (Alan OCallaghan) — Wed, 20 May 2026 13:26:24 GMT

A collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control and visualization.

[bioc-release] COTAN 2.12.1

silvia.galfre@di.unipi.it (Galfrè Silvia Giulia) — Wed, 20 May 2026 13:09:00 GMT

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

[bioc-release] StatescopeR 1.0.1

m.f.b.steketee@amsterdamumc.nl (Mischa Steketee) — Wed, 20 May 2026 08:46:00 GMT

StatescopeR is an R wrapper around Statescope, a computational framework designed to discover cell states from cell type-specific gene expression profiles inferred from bulk RNA profiles.

[bioc-release] GSVA 2.6.2

robert.castelo@upf.edu (Robert Castelo) — Tue, 19 May 2026 17:26:43 GMT

Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner.

[bioc-release] scrapper 1.6.3

infinite.monkeys.with.keyboards@gmail.com (Aaron Lun) — Tue, 19 May 2026 10:09:14 GMT

Implements R bindings to C++ code for analyzing single-cell (expression) data, mostly from various libscran libraries. Each function performs an individual step in the single-cell analysis workflow, ranging from quality control to clustering and marker detection. Additional wrappers are provided for easy construction of end-to-end workflows involving Bioconductor objects like SingleCellExperiments.

[bioc-release] imcRtools 1.18.1

daniel.schulz@uzh.ch (Daniel Schulz) — Tue, 19 May 2026 07:03:52 GMT

This R package supports the handling and analysis of imaging mass cytometry and other highly multiplexed imaging data. The main functionality includes reading in single-cell data after image segmentation and measurement, data formatting to perform channel spillover correction and a number of spatial analysis approaches. First, cell-cell interactions are detected via spatial graph construction; these graphs can be visualized with cells representing nodes and interactions representing edges. Furthermore, per cell, its direct neighbours are summarized to allow spatial clustering. Per image/grouping level, interactions between types of cells are counted, averaged and compared against random permutations. In that way, types of cells that interact more (attraction) or less (avoidance) frequently than expected by chance are detected.

[bioc-release] SEMPLR 1.0.1

kenney.grace6@gmail.com (Grace Kenney) — Mon, 18 May 2026 19:21:04 GMT

SEMPLR computes transcription factor binding affinity scores for genomic positions and genetic variants. Scores are computed from SNP Effect Matrices (SEMs) produced by SEMpl. 223 pre-computed SEMs are included with the package or custom sets can be provided. Enrichment can be tested among sets of genomic positions to determine if transcription factor binding events occur more often than expected. Comparing binding affinity scores between alleles can reveal differences in transcription factor binding with genetic variation. This package also includes several visualization functions to view scores both on the motif and variant/position level.

[bioc-release] BatChef 1.0.1

elena.zuin.3@phd.unipd.it (Elena Zuin) — Mon, 18 May 2026 16:26:59 GMT

This package implements a variety of methods for batch correction in single-cell RNA sequencing (scRNA-seq) data. It incorporates quantitative metrics (e.g. Wasserstein distance, Adjusted Rand Index) to evaluate their performance. Furthermore, the package assists users in identifying and applying the optimal method for specific datasets.

[bioc-release] ggsc 1.10.1

guangchuangyu@gmail.com (Guangchuang Yu) — Sun, 17 May 2026 09:05:54 GMT

Useful functions to visualize single cell and spatial data. It supports visualizing 'Seurat', 'SingleCellExperiment' and 'SpatialExperiment' objects through grammar of graphics syntax implemented in 'ggplot2'.

[bioc-release] gdsfmt 1.48.1

zhengx@u.washington.edu (Xiuwen Zheng) — Fri, 15 May 2026 06:29:46 GMT

Provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files. GDS is portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited for large-scale datasets, especially for data which are much larger than the available random-access memory. The gdsfmt package offers the efficient operations specifically designed for integers of less than 8 bits, since a diploid genotype, like single-nucleotide polymorphism (SNP), usually occupies fewer bits than a byte. Data compression and decompression are available with relatively efficient random access. It is also allowed to read a GDS file in parallel with multiple R processes supported by the package parallel.

[bioc-release] BiocPkgTools 1.30.0

seandavi@gmail.com (Sean Davis) — Thu, 14 May 2026 20:07:28 GMT

Bioconductor has a rich ecosystem of metadata around packages, usage, and build status. This package is a simple collection of functions to access that metadata from R. The goal is to expose metadata for data mining and value-added functionality such as package searching, text mining, and analytics on packages.

[bioc-release] splicelogic 1.0.1

beatrizcampillo29@gmail.com (Beatriz Campillo) — Thu, 14 May 2026 15:31:14 GMT

Translate differential transcript usage results into discrete splice events.

[bioc-release] BiocGenerics 0.58.1

hpages.on.github@gmail.com (Hervé Pagès) — Thu, 14 May 2026 04:52:20 GMT

The package defines many S4 generic functions used in Bioconductor.

[bioc-release] CyTOFpower 1.18.1

anne-maud.ferreira@epfedu.fr (Anne-Maud Ferreira) — Wed, 13 May 2026 19:13:05 GMT

This package is a tool to predict the power of CyTOF experiments in the context of differential state analyses. The package provides a shiny app with two options to predict the power of an experiment: i. generation of in-sicilico CyTOF data, using users input ii. browsing in a grid of parameters for which the power was already precomputed.

[bioc-release] spatialHeatmap 2.18.2

jzhan067@ucr.edu (Jianhai Zhang) — Wed, 13 May 2026 03:58:24 GMT

The spatialHeatmap package offers the primary functionality for visualizing cell-, tissue- and organ-specific assay data in spatial anatomical images. Additionally, it provides extended functionalities for large-scale data mining routines and co-visualizing bulk and single-cell data. A description of the project is available here: https://spatialheatmap.org.

[bioc-release] epigraHMM 1.20.2

pedrobaldoni@gmail.com (Pedro Baldoni) — Tue, 12 May 2026 23:41:15 GMT

epigraHMM provides a set of tools for the analysis of epigenomic data based on hidden Markov Models. It contains two separate peak callers, one for consensus peaks from biological or technical replicates, and one for differential peaks from multi-replicate multi-condition experiments. In differential peak calling, epigraHMM provides window-specific posterior probabilities associated with every possible combinatorial pattern of read enrichment across conditions.