Packages
655 packages on Bioconductor tagged SingleCell or Genetics or BSgenome, most distinct IPs first
SingleCell, Genetics and BSgenome 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| scDblFinder scDblFinderPierre-Luc Germain | Pierre-Luc Germain | software | 14 Oct 2026 | 6,116 | 121 |
| batchelor Single-Cell Batch Correction MethodsAaron Lun | Aaron Lun | software | 28 Apr 2026 | 5,720 | 56 |
| pathview a tool set for pathway based data integration and visualizationWeijun Luo | Weijun Luo | software | 28 Apr 2026 | 5,706 | 50 |
| 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 |
| DECIPHER Tools for curating, analyzing, and manipulating biological sequencesErik Wright | Erik Wright | software | 30 Jul 2026 | 4,882 | 16 |
| slingshot Tools for ordering single-cell sequencingKelly Street | Kelly Street | software | 28 Apr 2026 | 4,684 | 38 |
| TrajectoryUtils Single-Cell Trajectory Analysis UtilitiesAaron Lun | Aaron Lun | software | 28 Apr 2026 | 4,611 | 35 |
| 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 |
| zellkonverter Conversion Between scRNA-seq ObjectsLuke Zappia | Luke Zappia | software | 29 Apr 2026 | 4,278 | 41 |