Packages
872 packages on Bioconductor tagged SingleCell or Genetics or GeneSetEnrichment, most distinct IPs first
SingleCell, Genetics and GeneSetEnrichment in Topics
| Package | Maintainer | Category | Latest version | Distinct IPs a month | Needs |
|---|---|---|---|---|---|
| Biostrings Efficient manipulation of biological stringsHervé Pagès | Hervé Pagès | software | 2 Sep 2026 | 58,962 | 14 |
| GenomicRanges Representation and manipulation of genomic intervalsHervé Pagès | Hervé Pagès | software | 28 Apr 2026 | 56,974 | 10 |
| SummarizedExperiment A container (S4 class) for matrix-like assaysHervé Pagès | Hervé Pagès | software | 28 Apr 2026 | 53,484 | 24 |
| limma Linear Models for Microarray and Omics DataGordon Smyth | Gordon Smyth | software | 10 Aug 2026 | 45,965 | 6 |
| GenomeInfoDb Utilities for manipulating chromosome names, including modifying them to follow a particular naming styleHervé Pagès | Hervé Pagès | software | 28 Apr 2026 | 37,356 | 20 |
| edgeR Empirical Analysis of Digital Gene Expression Data in RYunshun Chen | Yunshun Chen | software | 19 Oct 2026 | 32,392 | 10 |
| enrichplot Visualization of Functional Enrichment ResultGuangchuang Yu | Guangchuang Yu | software | 28 Sep 2026 | 30,370 | 128 |
| clusterProfiler A Universal Enrichment Tool for Interpreting Omics DataGuangchuang Yu | Guangchuang Yu | software | 19 Oct 2026 | 29,661 | 138 |
| DOSE Disease Ontology Semantic and Enrichment analysisGuangchuang Yu | Guangchuang Yu | software | 28 Apr 2026 | 28,873 | 77 |
| fgsea Fast Gene Set Enrichment AnalysisAlexey Sergushichev | Alexey Sergushichev | software | 28 Apr 2026 | 28,660 | 38 |
| GenomicAlignments Representation and manipulation of short genomic alignmentsHervé Pagès | Hervé Pagès | software | 28 Apr 2026 | 27,006 | 41 |
| 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 |
| assorthead Assorted Header-Only C++ LibrariesAaron Lun | Aaron Lun | software | 8 Oct 2026 | 19,436 | 0 |
| GenomicFeatures Query the gene models of a given organism/assemblyH. Pagès | H. Pagès | software | 28 Apr 2026 | 19,218 | 74 |
| BSgenome Software infrastructure for efficient representation of full genomes and their SNPsHervé Pagès | Hervé Pagès | software | 28 Apr 2026 | 14,375 | 57 |
| scuttle Legacy Utilities for Single-Cell RNA-Seq AnalysisAaron Lun | Aaron Lun | software | 28 Apr 2026 | 14,236 | 39 |
| GSEABase Gene set enrichment data structures and methodsBioconductor Package Maintainer | Bioconductor Package Maintainer | software | 28 Apr 2026 | 13,344 | 46 |
| GSVA Gene Set Variation Analysis for Microarray and RNA-Seq DataRobert Castelo | Robert Castelo | software | 25 Oct 2026 | 12,758 | 97 |
| 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 |
| bluster Clustering Algorithms for BioconductorAaron Lun | Aaron Lun | software | 28 Apr 2026 | 10,903 | 44 |
| SpatialExperiment S4 Class for Spatially Resolved -omics DataDario Righelli | Dario Righelli | software | 28 Apr 2026 | 10,718 | 64 |
| scran Methods for Single-Cell RNA-Seq Data AnalysisAaron Lun | Aaron Lun | software | 28 Apr 2026 | 10,139 | 62 |
| VariantAnnotation Annotation of Genetic VariantsBioconductor Package Maintainer | Bioconductor Package Maintainer | software | 28 Apr 2026 | 9,664 | 76 |
| pwalign Perform pairwise sequence alignmentsHervé Pagès | Hervé Pagès | software | 28 Apr 2026 | 9,392 | 15 |
| glmGamPoi Fit a Gamma-Poisson Generalized Linear ModelConstantin Ahlmann-Eltze | Constantin Ahlmann-Eltze | software | 28 Apr 2026 | 7,000 | 46 |
| SingleR Reference-Based Single-Cell RNA-Seq AnnotationAaron Lun | Aaron Lun | software | 10 Sep 2026 | 6,761 | 28 |
| ReactomePA Reactome Pathway AnalysisGuangchuang Yu | Guangchuang Yu | software | 28 Apr 2026 | 6,720 | 141 |
| 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 |