Packages

1,226 packages on Bioconductor tagged AnnotationData or Transcription or GraphAndNetwork, most distinct IPs first

AnnotationData, Transcription and GraphAndNetwork 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
graph graph: A package to handle graph data structuresBioconductor Package Maintainer	Bioconductor Package Maintainer	software	28 Apr 2026	25,655	7
org.Mm.eg.db Genome wide annotation for MouseBioconductor Package Maintainer	Bioconductor Package Maintainer	annotation	no date on record	13,520	42
GSEABase Gene set enrichment data structures and methodsBioconductor Package Maintainer	Bioconductor Package Maintainer	software	28 Apr 2026	13,344	46
Rgraphviz Provides plotting capabilities for R graph objectsKasper Daniel Hansen	Kasper Daniel Hansen	software	28 Apr 2026	11,263	10
ensembldb Utilities to create and use Ensembl-based annotation databasesJohannes Rainer	Johannes Rainer	software	25 May 2026	11,000	80
RBGL An interface to the BOOST graph libraryBioconductor Package Maintainer	Bioconductor Package Maintainer	software	28 Apr 2026	10,698	9
EnhancedVolcano Publication-ready volcano plots with enhanced colouring and labelingJared Andrews	Jared Andrews	software	28 Apr 2026	7,620	25
reactome.db A set of annotation maps for reactomeWillem Ligtenberg	Willem Ligtenberg	annotation	no date on record	7,578	42
graphite GRAPH Interaction from pathway Topological EnvironmentGabriele Sales	Gabriele Sales	software	28 Apr 2026	7,012	48
KEGGgraph KEGGgraph: A graph approach to KEGG PATHWAY in R and BioconductorJitao David Zhang	Jitao David Zhang	software	28 Apr 2026	6,807	14
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
tximport Import and summarize transcript-level estimates for transcript- and gene-level analysisMichael Love	Michael Love	software	28 Apr 2026	5,804	3
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
TFBSTools Software Package for Transcription Factor Binding Site (TFBS) AnalysisGe Tan	Ge Tan	software	28 Apr 2026	4,721	79
AUCell AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)Gert Hulselmans	Gert Hulselmans	software	29 Apr 2026	4,610	115
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
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
IlluminaHumanMethylation450kanno.ilmn12.hg19 Annotation for Illumina's 450k methylation arraysKasper Daniel Hansen	Kasper Daniel Hansen	annotation	no date on record	2,852	144