Packages
85 packages on Bioconductor tagged SingleCell or SequencingData or ExperimentHub, most distinct IPs first
SingleCell, SequencingData and ExperimentHub in Topics
| Package | Maintainer | Category | Latest version | Distinct IPs a month | Needs |
|---|---|---|---|---|---|
| edgeR Empirical Analysis of Digital Gene Expression Data in RYunshun Chen | Yunshun Chen | software | 19 Oct 2026 | 32,392 | 10 |
| HDF5Array HDF5 datasets as array-like objects in RHervé Pagès | Hervé Pagès | software | 28 Apr 2026 | 20,537 | 28 |
| scater Single-Cell Analysis Toolkit for Gene Expression Data in RAlan O'Callaghan | Alan O'Callaghan | software | 2 Jul 2026 | 12,635 | 78 |
| scran Methods for Single-Cell RNA-Seq Data AnalysisAaron Lun | Aaron Lun | software | 28 Apr 2026 | 10,139 | 62 |
| 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 |
| Rsubread Mapping, quantification and variant analysis of sequencing dataWei Shi | Wei Shi | software | 28 Apr 2026 | 2,951 | 8 |
| airway RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014Michael Love | Michael Love | experiment | 5 May 2026 | 2,854 | 25 |
| scRNAseq Collection of Public Single-Cell RNA-Seq DatasetsAaron Lun | Aaron Lun | experiment | 5 May 2026 | 2,314 | 121 |
| pasilla Data package with per-exon and per-gene read counts of RNA-seq samples of Pasilla knock-down by Brooks et al., Genome Research 2011.Alejandro Reyes | Alejandro Reyes | experiment | 5 May 2026 | 1,554 | 108 |
| SC3 Single-Cell Consensus ClusteringVladimir Kiselev | Vladimir Kiselev | software | 28 Apr 2026 | 1,368 | 92 |
| tximportData tximportDataMichael Love | Michael Love | experiment | 5 May 2026 | 1,330 | 0 |
| clusterExperiment Compare Clusterings for Single-Cell SequencingElizabeth Purdom | Elizabeth Purdom | software | 28 Apr 2026 | 1,150 | 147 |
| Linnorm Linear model and normality based normalization and transformation method (Linnorm)Shun Hang Yip | Shun Hang Yip | software | 28 Apr 2026 | 1,088 | 62 |
| RNAseqData.HNRNPC.bam.chr14 Aligned reads from RNAseq experiment: Transcription profiling by high throughput sequencing of HNRNPC knockdown and control HeLa cellsHervé Pagès | Hervé Pagès | experiment | 5 May 2026 | 1,069 | 0 |
| TRONCO TRONCO, an R package for TRanslational ONCOlogyLuca De Sano | Luca De Sano | software | 28 Apr 2026 | 1,025 | 47 |
| SIMLR Single-cell Interpretation via Multi-kernel LeaRning (SIMLR)Luca De Sano | Luca De Sano | software | 28 Apr 2026 | 1,010 | 14 |
| pasillaBamSubset Subset of BAM files from "Pasilla" experimentHervé Pagès | Hervé Pagès | experiment | 5 May 2026 | 997 | 0 |
| GSVAdata Data employed in the vignette of the GSVA packageRobert Castelo | Robert Castelo | experiment | 28 Jul 2026 | 955 | 78 |
| immunoClust immunoClust - Automated Pipeline for Population Detection in Flow CytometryTill Soerensen | Till Soerensen | software | 28 Apr 2026 | 918 | 24 |
| curatedMetagenomicData Curated Metagenomic Data of the Human MicrobiomeLucas schiffer | Lucas schiffer | experiment | 5 May 2026 | 913 | 148 |
| ExpressionAtlas Download datasets from EMBL-EBI Expression AtlasAnil Thanki | Anil Thanki | software | 28 Apr 2026 | 827 | 64 |
| switchde Switch-like differential expression across single-cell trajectoriesKieran Campbell | Kieran Campbell | software | 28 Apr 2026 | 780 | 50 |
| zebrafishRNASeq Zebrafish RNA-Seq Experimental Data from Ferreira et al. (2014)Davide Risso | Davide Risso | experiment | 5 May 2026 | 702 | 0 |
| BPRMeth Model higher-order methylation profilesChantriolnt-Andreas Kapourani | Chantriolnt-Andreas Kapourani | software | no date on record | 606 | |
| yeastNagalakshmi Yeast genome RNA sequencing data based on Nagalakshmi et. al.Bioconductor Package Maintainer | Bioconductor Package Maintainer | experiment | 5 May 2026 | 587 | 0 |
| AneuFinder Analysis of Copy Number Variation in Single-Cell-Sequencing Data | no date on record | 584 | |||
| harbChIP Experimental Data Package: harbChIPVJ Carey | VJ Carey | experiment | 5 May 2026 | 581 | 16 |
| DMRcatedata Data Package for DMRcateTim Peters | Tim Peters | experiment | 5 May 2026 | 522 | 208 |
| parathyroidSE RangedSummarizedExperiment for RNA-Seq of primary cultures of parathyroid tumors by Haglund et al., J Clin Endocrinol Metab 2012. | no date on record | 464 |