Packages
520 packages on Bioconductor tagged SingleCell or QualityControl or ChIPSeq, most distinct IPs first
SingleCell, QualityControl and ChIPSeq 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 |
| 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 |
| Rsamtools Binary alignment (BAM), FASTA, variant call (BCF), and tabix file importBioconductor Package Maintainer | Bioconductor Package Maintainer | software | 28 Apr 2026 | 30,337 | 28 |
| 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 |
| 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 |
| 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 |
| ShortRead FASTQ input and manipulationBioconductor Package Maintainer | Bioconductor Package Maintainer | software | 28 Apr 2026 | 8,126 | 53 |
| 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 |
| 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 |
| MSnbase Base Functions and Classes for Mass Spectrometry and ProteomicsLaurent Gatto | Laurent Gatto | software | 9 Aug 2026 | 5,521 | 134 |
| 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 |
| monocle Clustering, differential expression, and trajectory analysis for single- cell RNA-SeqCole Trapnell | Cole Trapnell | software | 28 Apr 2026 | 4,485 | 74 |
| zellkonverter Conversion Between scRNA-seq ObjectsLuke Zappia | Luke Zappia | software | 29 Apr 2026 | 4,278 | 41 |
| DropletUtils Utilities for Handling Single-Cell Droplet DataJonathan Griffiths | Jonathan Griffiths | software | 27 Sep 2026 | 4,107 | 59 |
| minfi Analyze Illumina Infinium DNA methylation arraysKasper Daniel Hansen | Kasper Daniel Hansen | software | 28 Apr 2026 | 4,041 | 143 |
| ChIPseeker ChIPseeker for ChIP peak Annotation, Comparison, and VisualizationGuangchuang Yu | Guangchuang Yu | software | 28 Apr 2026 | 3,962 | 158 |
| UCell Rank-based signature enrichment analysis for single-cell dataMassimo Andreatta | Massimo Andreatta | software | 28 Apr 2026 | 3,924 | 41 |
| MAST Model-based Analysis of Single Cell TranscriptomicsAndrew McDavid | Andrew McDavid | software | 28 Apr 2026 | 3,740 | 56 |
| variancePartition Quantify and interpret drivers of variation in multilevel gene expression experimentsGabriel E. Hoffman | Gabriel E. Hoffman | software | 28 Apr 2026 | 3,211 | 99 |
| interactiveDisplayBase Base package for enabling powerful shiny web displays of Bioconductor objects | no date on record | 2,988 |