Packages
358 packages on Bioconductor, most distinct IPs first
| Package | Maintainer | Category | Latest version | Distinct IPs a month | Needs |
|---|---|---|---|---|---|
| S4Vectors Foundation of vector-like and list-like containers in BioconductorHervé Pagès | Hervé Pagès | software | 16 Sep 2026 | 74,754 | 7 |
| SparseArray High-performance sparse data representation and manipulation in RHervé Pagès | Hervé Pagès | software | 22 Sep 2026 | 59,629 | 19 |
| S4Arrays Foundation of array-like containers in BioconductorHervé Pagès | Hervé Pagès | software | 22 Sep 2026 | 53,675 | 14 |
| SummarizedExperiment A container (S4 class) for matrix-like assaysHervé Pagès | Hervé Pagès | software | 28 Apr 2026 | 53,484 | 24 |
| SingleCellExperiment S4 Classes for Single Cell DataDavide Risso | Davide Risso | software | 28 Apr 2026 | 24,483 | 25 |
| sparseMatrixStats Summary Statistics for Rows and Columns of Sparse MatricesConstantin Ahlmann-Eltze | Constantin Ahlmann-Eltze | software | 28 Apr 2026 | 21,500 | 11 |
| ScaledMatrix Creating a DelayedMatrix of Scaled and Centered ValuesAaron Lun | Aaron Lun | software | 28 Apr 2026 | 17,725 | 21 |
| 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 |
| 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 |
| 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 |
| 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 |
| siggenes Multiple Testing using SAM and Efron's Empirical Bayes ApproachesHolger Schwender | Holger Schwender | software | 28 Apr 2026 | 4,901 | 17 |
| slingshot Tools for ordering single-cell sequencingKelly Street | Kelly Street | software | 28 Apr 2026 | 4,684 | 38 |
| seqLogo Sequence logos for DNA sequence alignmentsRobert Ivanek | Robert Ivanek | software | 28 Apr 2026 | 4,602 | 4 |
| Spectra Spectra Infrastructure for Mass Spectrometry DataRforMassSpectrometry Package Maintainer | RforMassSpectrometry Package Maintainer | software | 9 Jun 2026 | 4,465 | 30 |
| STRINGdb STRINGdb - Protein-Protein Interaction Networks and Functional Enrichment AnalysisDamian Szklarczyk | Damian Szklarczyk | software | 27 Oct 2026 | 4,459 | 49 |
| snpStats SnpMatrix and XSnpMatrix classes and methodsDavid Clayton | David Clayton | software | 28 Apr 2026 | 3,488 | 12 |
| scrapper Bindings to C++ Libraries for Single-Cell AnalysisAaron Lun | Aaron Lun | software | 19 May 2026 | 3,119 | 30 |
| singscore Rank-based single-sample gene set scoring methodMalvika Kharbanda | Malvika Kharbanda | software | 28 Apr 2026 | 2,915 | 120 |
| SNPRelate Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP DataXiuwen Zheng | Xiuwen Zheng | software | 28 Apr 2026 | 2,810 | 3 |
| systemPipeR systemPipeR: A Multipurpose Workflow Management System for Reproducible Data AnalysisThomas Girke | Thomas Girke | software | 28 Apr 2026 | 2,506 | 94 |
| survcomp Performance Assessment and Comparison for Survival AnalysisBenjamin Haibe-Kains | Benjamin Haibe-Kains | software | 28 Apr 2026 | 2,383 | 55 |
| scRNAseq Collection of Public Single-Cell RNA-Seq DatasetsAaron Lun | Aaron Lun | experiment | 5 May 2026 | 2,314 | 121 |
| SeqArray Data management of large-scale whole-genome sequence variant calls using GDS filesXiuwen Zheng | Xiuwen Zheng | software | 31 May 2026 | 1,955 | 19 |
| simplifyEnrichment Simplify Functional Enrichment ResultsZuguang Gu | Zuguang Gu | software | 28 Apr 2026 | 1,854 | 92 |
| SPIA Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbationsAdi Laurentiu Tarca | Adi Laurentiu Tarca | software | 28 Apr 2026 | 1,839 | 15 |