Packages

1,038 packages on Bioconductor tagged AnnotationData or FunctionalGenomics, most distinct IPs first

AnnotationData and FunctionalGenomics 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
org.Hs.eg.db Genome wide annotation for HumanBioconductor Package Maintainer	Bioconductor Package Maintainer	annotation	no date on record	29,813	42
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
ensembldb Utilities to create and use Ensembl-based annotation databasesJohannes Rainer	Johannes Rainer	software	25 May 2026	11,000	80
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
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
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
decoupleR decoupleR: Ensemble of computational methods to infer biological activities from omics dataPau Badia-i-Mompel	Pau Badia-i-Mompel	software	30 Oct 2025	3,634	41
maftools Summarize, Analyze and Visualize MAF FilesAnand Mayakonda	Anand Mayakonda	software	28 Apr 2026	3,523	26
EnsDb.Hsapiens.v86 Ensembl based annotation packageJohannes Rainer	Johannes Rainer	annotation	no date on record	3,389	81
variancePartition Quantify and interpret drivers of variation in multilevel gene expression experimentsGabriel E. Hoffman	Gabriel E. Hoffman	software	28 Apr 2026	3,211	99
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
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
DiffBind Differential Binding Analysis of ChIP-Seq Peak DataRory Stark	Rory Stark	software	21 Jul 2026	2,490	141
tximeta Transcript Quantification Import with Automatic MetadataMichael Love	Michael Love	software	26 Oct 2026	2,485	108
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
JASPAR2020 Data package for JASPAR database (version 2020)Damir Baranasic	Damir Baranasic	annotation	no date on record	2,154	1
BSgenome.Mmusculus.UCSC.mm10 Full genome sequences for Mus musculus (UCSC version mm10, based on GRCm38.p6)Bioconductor Package Maintainer	Bioconductor Package Maintainer	annotation	no date on record	2,152	58
miloR Differential neighbourhood abundance testing on a graphMike Morgan	Mike Morgan	software	12 May 2026	2,130	101
hgu133a.db Affymetrix Affymetrix HG-U133A Array annotation data (chip hgu133a)Bioconductor Package Maintainer	Bioconductor Package Maintainer	annotation	no date on record	1,996	43
org.At.tair.db Genome wide annotation for ArabidopsisBioconductor Package Maintainer	Bioconductor Package Maintainer	annotation	no date on record	1,861	42