Packages

968 packages on Bioconductor tagged AnnotationData or ExperimentHub or RNASeq, most distinct IPs first

AnnotationData, ExperimentHub and RNASeq in Topics

Package	Maintainer	Category	Latest version	Distinct IPs a month	Needs
limma Linear Models for Microarray and Omics DataGordon Smyth	Gordon Smyth	software	10 Aug 2026	45,965	6
GenomeInfoDbData Species and taxonomy ID look up tables used by GenomeInfoDbBioconductor Maintainer	Bioconductor Maintainer	annotation	no date on record	36,797	0
GO.db A set of annotation maps describing the entire Gene OntologyBioconductor Package Maintainer	Bioconductor Package Maintainer	annotation	no date on record	33,694	42
edgeR Empirical Analysis of Digital Gene Expression Data in RYunshun Chen	Yunshun Chen	software	19 Oct 2026	32,392	10
DESeq2 Differential gene expression analysis based on the negative binomial distributionMichael Love	Michael Love	software	28 Apr 2026	32,072	54
org.Hs.eg.db Genome wide annotation for HumanBioconductor Package Maintainer	Bioconductor Package Maintainer	annotation	no date on record	29,813	42
GenomicAlignments Representation and manipulation of short genomic alignmentsHervé Pagès	Hervé Pagès	software	28 Apr 2026	27,006	41
org.Mm.eg.db Genome wide annotation for MouseBioconductor Package Maintainer	Bioconductor Package Maintainer	annotation	no date on record	13,520	42
GSVA Gene Set Variation Analysis for Microarray and RNA-Seq DataRobert Castelo	Robert Castelo	software	25 Oct 2026	12,758	97
sva Surrogate Variable AnalysisJeffrey T. Leek	Jeffrey T. Leek	software	5 May 2026	10,804	68
reactome.db A set of annotation maps for reactomeWillem Ligtenberg	Willem Ligtenberg	annotation	no date on record	7,578	42
TxDb.Hsapiens.UCSC.hg19.knownGene Annotation package for TxDb object(s)Bioconductor Package Maintainer	Bioconductor Package Maintainer	annotation	no date on record	6,258	75
pathview a tool set for pathway based data integration and visualizationWeijun Luo	Weijun Luo	software	28 Apr 2026	5,706	50
HDO.db A set of annotation maps describing the entire Human Disease OntologyErqiang Hu	Erqiang Hu	annotation	no date on record	5,277	42
BSgenome.Hsapiens.UCSC.hg38 Full genomic sequences for Homo sapiens (UCSC genome hg38)Bioconductor Package Maintainer	Bioconductor Package Maintainer	annotation	no date on record	4,989	60
monocle Clustering, differential expression, and trajectory analysis for single- cell RNA-SeqCole Trapnell	Cole Trapnell	software	28 Apr 2026	4,485	74
hgu133plus2.db Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data (chip hgu133plus2)Bioconductor Package Maintainer	Bioconductor Package Maintainer	annotation	no date on record	4,227	43
TxDb.Hsapiens.UCSC.hg38.knownGene Annotation package for TxDb object(s)Bioconductor Package Maintainer	Bioconductor Package Maintainer	annotation	no date on record	3,919	75
EnsDb.Hsapiens.v86 Ensembl based annotation packageJohannes Rainer	Johannes Rainer	annotation	no date on record	3,389	81
org.Rn.eg.db Genome wide annotation for RatBioconductor Package Maintainer	Bioconductor Package Maintainer	annotation	no date on record	3,202	42
interactiveDisplayBase Base package for enabling powerful shiny web displays of Bioconductor objects			no date on record	2,988
Rsubread Mapping, quantification and variant analysis of sequencing dataWei Shi	Wei Shi	software	28 Apr 2026	2,951	8
IlluminaHumanMethylation450kanno.ilmn12.hg19 Annotation for Illumina's 450k methylation arraysKasper Daniel Hansen	Kasper Daniel Hansen	annotation	no date on record	2,852	144
BSgenome.Hsapiens.UCSC.hg19 Full genome sequences for Homo sapiens (UCSC version hg19, based on GRCh37.p13)Bioconductor Package Maintainer	Bioconductor Package Maintainer	annotation	no date on record	2,842	58
DEXSeq Inference of differential exon usage in RNA-SeqHugo Gruson	Hugo Gruson	software	28 Apr 2026	2,837	107
EDASeq Exploratory Data Analysis and Normalization for RNA-SeqDavide Risso	Davide Risso	software	28 Apr 2026	2,602	111
ALDEx2 Analysis Of Differential Abundance Taking Sample and Scale Variation Into AccountGreg Gloor	Greg Gloor	software	28 Apr 2026	2,533	56
systemPipeR systemPipeR: A Multipurpose Workflow Management System for Reproducible Data AnalysisThomas Girke	Thomas Girke	software	28 Apr 2026	2,506	94
goseq Gene Ontology analyser for RNA-seq and other length biased dataFederico Marini	Federico Marini	software	28 Apr 2026	2,404	104
TxDb.Mmusculus.UCSC.mm10.knownGene Annotation package for TxDb object(s)Bioconductor Package Maintainer	Bioconductor Package Maintainer	annotation	no date on record	2,192	75