Packages
619 packages on Bioconductor tagged SingleCell or SequencingData or Preprocessing, most distinct IPs first
SingleCell, SequencingData and Preprocessing 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 |
| 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 |
| sva Surrogate Variable AnalysisJeffrey T. Leek | Jeffrey T. Leek | software | 5 May 2026 | 10,804 | 68 |
| SpatialExperiment S4 Class for Spatially Resolved -omics DataDario Righelli | Dario Righelli | software | 28 Apr 2026 | 10,718 | 64 |
| affy Methods for Affymetrix Oligonucleotide ArraysRobert D. Shear | Robert D. Shear | software | 28 Apr 2026 | 10,556 | 11 |
| scran Methods for Single-Cell RNA-Seq Data AnalysisAaron Lun | Aaron Lun | software | 28 Apr 2026 | 10,139 | 62 |
| vsn Variance stabilization and calibration for microarray dataWolfgang Huber | Wolfgang Huber | software | 28 Apr 2026 | 7,536 | 33 |
| 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 |
| biovizBase Basic graphic utilities for visualization of genomic data.Michael Lawrence | Michael Lawrence | software | 28 Apr 2026 | 6,487 | 126 |
| scDblFinder scDblFinderPierre-Luc Germain | Pierre-Luc Germain | software | 14 Oct 2026 | 6,116 | 121 |
| tximport Import and summarize transcript-level estimates for transcript- and gene-level analysisMichael Love | Michael Love | software | 28 Apr 2026 | 5,804 | 3 |
| batchelor Single-Cell Batch Correction MethodsAaron Lun | Aaron Lun | software | 28 Apr 2026 | 5,720 | 56 |
| celldex Index of Reference Cell Type DatasetsAaron Lun | Aaron Lun | experiment | 5 May 2026 | 5,717 | 95 |
| 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 |
| DropletUtils Utilities for Handling Single-Cell Droplet DataJonathan Griffiths | Jonathan Griffiths | software | 27 Sep 2026 | 4,107 | 59 |
| oligo Preprocessing tools for oligonucleotide arraysBenilton Carvalho | Benilton Carvalho | software | 28 Apr 2026 | 4,087 | 52 |
| minfi Analyze Illumina Infinium DNA methylation arraysKasper Daniel Hansen | Kasper Daniel Hansen | software | 28 Apr 2026 | 4,041 | 143 |
| UCell Rank-based signature enrichment analysis for single-cell dataMassimo Andreatta | Massimo Andreatta | software | 28 Apr 2026 | 3,924 | 41 |
| cytolib C++ infrastructure for representing and interacting with the gated cytometry dataMike Jiang | Mike Jiang | software | 28 Apr 2026 | 3,820 | 8 |
| MAST Model-based Analysis of Single Cell TranscriptomicsAndrew McDavid | Andrew McDavid | software | 28 Apr 2026 | 3,740 | 56 |
| HSMMSingleCell Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)Cole Trapnell | Cole Trapnell | experiment | 5 May 2026 | 3,553 | 0 |