Packages

1,004 packages on Bioconductor tagged SingleCell or Transcriptomics or AnnotationData, most distinct IPs first

SingleCell, Transcriptomics and AnnotationData 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
SingleCellExperiment S4 Classes for Single Cell DataDavide Risso	Davide Risso	software	28 Apr 2026	24,483	25
HDF5Array HDF5 datasets as array-like objects in RHervé Pagès	Hervé Pagès	software	28 Apr 2026	20,537	28
org.Mm.eg.db Genome wide annotation for MouseBioconductor Package Maintainer	Bioconductor Package Maintainer	annotation	no date on record	13,520	42
scater Single-Cell Analysis Toolkit for Gene Expression Data in RAlan O'Callaghan	Alan O'Callaghan	software	2 Jul 2026	12,635	78
ensembldb Utilities to create and use Ensembl-based annotation databasesJohannes Rainer	Johannes Rainer	software	25 May 2026	11,000	80
scran Methods for Single-Cell RNA-Seq Data AnalysisAaron Lun	Aaron Lun	software	28 Apr 2026	10,139	62
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
tximport Import and summarize transcript-level estimates for transcript- and gene-level analysisMichael Love	Michael Love	software	28 Apr 2026	5,804	3
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
slingshot Tools for ordering single-cell sequencingKelly Street	Kelly Street	software	28 Apr 2026	4,684	38
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
DropletUtils Utilities for Handling Single-Cell Droplet DataJonathan Griffiths	Jonathan Griffiths	software	27 Sep 2026	4,107	59
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
MAST Model-based Analysis of Single Cell TranscriptomicsAndrew McDavid	Andrew McDavid	software	28 Apr 2026	3,740	56
EnsDb.Hsapiens.v86 Ensembl based annotation packageJohannes Rainer	Johannes Rainer	annotation	no date on record	3,389	81
topGO Enrichment Analysis for Gene OntologyFederico Marini	Federico Marini	software	28 Apr 2026	3,228	48
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
ropls PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics dataEtienne A. Thevenot	Etienne A. Thevenot	software	28 Apr 2026	2,969	97
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