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[bioc] AnnotationHub 4.3.3

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Fri, 23 Oct 2026 13:26:26 GMT

This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access.

[bioc] Category 2.79.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 20 Oct 2026 03:29:27 GMT

A collection of tools for performing category (gene set enrichment) analysis.

[bioc] AnnotationDbi 1.75.2

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Thu, 27 Aug 2026 01:54:04 GMT

Implements a user-friendly interface for querying SQLite-based annotation data packages.

[bioc] ExperimentHub 3.3.2

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Wed, 12 Aug 2026 16:08:44 GMT

This package provides a client for the Bioconductor ExperimentHub web resource. ExperimentHub provides a central location where curated data from experiments, publications or training courses can be accessed. Each resource has associated metadata, tags and date of modification. The client creates and manages a local cache of files retrieved enabling quick and reproducible access.

[bioc] Biobase 2.73.2

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Jul 2026 23:32:39 GMT

Functions that are needed by many other packages or which replace R functions.

[bioc] VariantAnnotation 1.59.4

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Fri, 24 Jul 2026 10:23:12 GMT

Annotate variants, compute amino acid coding changes, predict coding outcomes.

[bioc] KEGGREST 1.53.6

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Wed, 22 Jul 2026 20:09:17 GMT

A package that provides a client interface to the Kyoto Encyclopedia of Genes and Genomes (KEGG) REST API. Only for academic use by academic users belonging to academic institutions (see ). Note that KEGGREST is based on KEGGSOAP by J. Zhang, R. Gentleman, and Marc Carlson, and KEGG (python package) by Aurelien Mazurie.

[bioc] biocViews 1.81.1

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 07 Jul 2026 21:48:36 GMT

Infrastructure to support 'views' used to classify Bioconductor packages. 'biocViews' are directed acyclic graphs of terms from a controlled vocabulary. There are three major classifications, corresponding to 'software', 'annotation', and 'experiment data' packages.

[bioc] ShortRead 1.71.1

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Sat, 04 Jul 2026 16:59:11 GMT

This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.

[bioc] ExperimentHubData 1.39.1

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Fri, 22 May 2026 22:20:44 GMT

Functions to add metadata to ExperimentHub db and resource files to AWS S3 buckets.

[bioc] OrganismDbi 1.55.1

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 23:43:16 GMT

The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.

[bioc] Bioc.gff 1.3.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 13:05:23 GMT

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.

[bioc] LoomExperiment 1.31.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:49:10 GMT

The LoomExperiment package provide a means to easily convert the Bioconductor "Experiment" classes to loom files and vice versa.

[bioc] BiocVersion 3.24.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:48:02 GMT

This package provides repository information for the appropriate version of Bioconductor.

[bioc] AnnotationFilter 1.37.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:45:23 GMT

This package provides class and other infrastructure to implement filters for manipulating Bioconductor annotation resources. The filters will be used by ensembldb, Organism.dplyr, and other packages.

[bioc] variants 1.37.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:43:22 GMT

Read and write VCF files. Identify structural location of variants and compute amino acid coding changes for non-synonymous variants. Use SIFT and PolyPhen database packages to predict consequence of amino acid coding changes.

[bioc] sequencing 1.37.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:43:15 GMT

Bioconductor enables the analysis and comprehension of high- throughput genomic data. We have a vast number of packages that allow rigorous statistical analysis of large data while keeping technological artifacts in mind. Bioconductor helps users place their analytic results into biological context, with rich opportunities for visualization. Reproducibility is an important goal in Bioconductor analyses. Different types of analysis can be carried out using Bioconductor, for example; Sequencing : RNASeq, ChIPSeq, variants, copy number etc.; Microarrays: expression, SNP, etc.; Domain specific analysis : Flow cytometry, Proteomics etc. For these analyses, one typically imports and works with diverse sequence-related file types, including fasta, fastq, BAM, gtf, bed, and wig files, among others. Bioconductor packages support import, common and advanced sequence manipulation operations such as trimming, transformation, and alignment including quality assessment.

[bioc] AnnotationHubData 1.43.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:41:49 GMT

These recipes convert a wide variety and a growing number of public bioinformatic data sets into easily-used standard Bioconductor data structures.

[bioc] liftOver 1.37.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:40:35 GMT

The liftOver facilities developed in conjunction with the UCSC browser track infrastructure are available for transforming data in GRanges formats. This is illustrated here with an image of the EBI/NHGRI GWAS catalog that is, as of May 10 2017, distributed with coordinates defined by NCBI build hg38.

[bioc] highthroughputassays 1.37.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:40:33 GMT

The workflow illustrates use of the flow cytometry packages to load, transform and visualize the flow data and gate certain populations in the dataset. The workflow loads the `flowCore`, `flowStats` and `flowWorkspace` packages and its dependencies. It loads the ITN data with 15 samples, each of which includes, in addition to FSC and SSC, 5 fluorescence channels: CD3, CD4, CD8, CD69 and HLADR.

[bioc] generegulation 1.37.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:40:31 GMT

The binding of transcription factor proteins (TFs) to DNA promoter regions upstream of gene transcription start sites (TSSs) is one of the most important mechanisms by which gene expression, and thus many cellular processes, are controlled. Though in recent years many new kinds of data have become available for identifying transcription factor binding sites (TFBSs) -- ChIP-seq and DNase I hypersensitivity regions among them -- sequence matching continues to play an important role. In this workflow we demonstrate Bioconductor techniques for finding candidate TF binding sites in DNA sequence using the model organism Saccharomyces cerevisiae. The methods demonstrated here apply equally well to other organisms.

[bioc] arrays 1.39.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:40:19 GMT

Using Bioconductor for Microarray Analysis workflow

[bioc] annotation 1.37.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:40:17 GMT

Annotation resources make up a significant proportion of the Bioconductor project. And there are also a diverse set of online resources available which are accessed using specific packages. This walkthrough will describe the most popular of these resources and give some high level examples on how to use them.

[bioc] GenomicFiles 1.49.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:39:03 GMT

This package provides infrastructure for parallel computations distributed 'by file' or 'by range'. User defined MAPPER and REDUCER functions provide added flexibility for data combination and manipulation.

[bioc] BiocStyle 2.41.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:37:53 GMT

Provides standard formatting styles for Bioconductor PDF and HTML documents. Package vignettes illustrate use and functionality.

[bioc] AnnotationForge 1.55.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:36:38 GMT

Provides code for generating Annotation packages and their databases. Packages produced are intended to be used with AnnotationDbi.

[bioc] Rsamtools 2.29.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:34:32 GMT

This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.

[bioc] chipseq 1.63.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:33:59 GMT

Tools for helping process short read data for chipseq experiments.

[bioc] GSEABase 1.75.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:32:25 GMT

This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).

[bioc] GeneMeta 1.85.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:31:13 GMT

A collection of meta-analysis tools for analysing high throughput experimental data

[bioc] hypergraph 1.85.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:31:10 GMT

A package that implements some simple capabilities for representing and manipulating hypergraphs.

[bioc] TENxBrainData 1.33.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:30:55 GMT

Single-cell RNA-seq data for 1.3 million brain cells from E18 mice, generated by 10X Genomics.

[bioc] CoCiteStats 1.85.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:30:54 GMT

A collection of software tools for dealing with co-citation data.

[bioc] bioDist 1.85.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:30:53 GMT

A collection of software tools for calculating distance measures.

[bioc] GOstats 2.79.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:30:38 GMT

A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations.

[bioc] Icens 1.85.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:30:28 GMT

Many functions for computing the NPMLE for censored and truncated data.

[bioc] RBGL 1.89.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:30:19 GMT

A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library.

[bioc] gpls 1.85.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:30:15 GMT

Classification using generalized partial least squares for two-group and multi-group (more than 2 group) classification.

[bioc] graph 1.91.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:30:05 GMT

A package that implements some simple graph handling capabilities.

[bioc] geneplotter 1.91.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:29:56 GMT

Functions for plotting genomic data

[bioc] genefilter 1.95.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:29:55 GMT

Some basic functions for filtering genes.

[bioc] annotate 1.91.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:29:54 GMT

Using R enviroments for annotation.

[bioc] DynDoc 1.91.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:29:53 GMT

A set of functions to create and interact with dynamic documents and vignettes.

[bioc] GSE62944 1.41.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:29:18 GMT

TCGA processed RNA-Seq data for 9264 tumor and 741 normal samples across 24 cancer types and made them available as GEO accession [GSE62944](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944). GSE62944 data have been parsed into a SummarizedExperiment object available in ExperimentHub.

[bioc] yeastNagalakshmi 1.49.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:24:07 GMT

The yeast genome data was retrieved from the sequence read archive, aligned with bwa, and converted to BAM format with samtools.

[bioc] hgu2beta7 1.53.0

maintainer@bioconductor.org (Bioconductor Package Maintainer) — Tue, 28 Apr 2026 12:21:58 GMT

Annotation data file for hgu2beta7 assembled using data from public data repositories