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Topic: SingleCell or SequencingData or FunctionalGenomics

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Release: Release 3.4 (2016)

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109 packages on Bioconductor tagged SingleCell or SequencingData or FunctionalGenomics, most distinct IPs first

SingleCell, SequencingData and FunctionalGenomics in Topics

PackageMaintainerCategoryLatest versionDistinct IPs a monthNeeds
limma
Linear Models for Microarray and Omics DataGordon Smyth		Gordon Smythsoftware10 Aug 202645,9656
edgeR
Empirical Analysis of Digital Gene Expression Data in RYunshun Chen		Yunshun Chensoftware19 Oct 202632,39210
HDF5Array
HDF5 datasets as array-like objects in RHervé Pagès		Hervé Pagèssoftware28 Apr 202620,53728
GSVA
Gene Set Variation Analysis for Microarray and RNA-Seq DataRobert Castelo		Robert Castelosoftware25 Oct 202612,75897
scater
Single-Cell Analysis Toolkit for Gene Expression Data in RAlan O'Callaghan		Alan O'Callaghansoftware2 Jul 202612,63578
scran
Methods for Single-Cell RNA-Seq Data AnalysisAaron Lun		Aaron Lunsoftware28 Apr 202610,13962
MAST
Model-based Analysis of Single Cell TranscriptomicsAndrew McDavid		Andrew McDavidsoftware28 Apr 20263,74056
HSMMSingleCell
Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)Cole Trapnell		Cole Trapnellexperiment5 May 20263,5530
maftools
Summarize, Analyze and Visualize MAF FilesAnand Mayakonda		Anand Mayakondasoftware28 Apr 20263,52326
variancePartition
Quantify and interpret drivers of variation in multilevel gene expression experimentsGabriel E. Hoffman		Gabriel E. Hoffmansoftware28 Apr 20263,21199
Rsubread
Mapping, quantification and variant analysis of sequencing dataWei Shi		Wei Shisoftware28 Apr 20262,9518
airway
RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014Michael Love		Michael Loveexperiment5 May 20262,85425
DiffBind
Differential Binding Analysis of ChIP-Seq Peak DataRory Stark		Rory Starksoftware21 Jul 20262,490141
scRNAseq
Collection of Public Single-Cell RNA-Seq DatasetsAaron Lun		Aaron Lunexperiment5 May 20262,314121
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 Reyesexperiment5 May 20261,554108
annotatr
Annotation of Genomic Regions to Genomic AnnotationsRaymond G. Cavalcante		Raymond G. Cavalcantesoftware27 Sep 20261,482118
hpar
Human Protein Atlas in RLaurent Gatto		Laurent Gattosoftware28 Apr 20261,38264
SC3
Single-Cell Consensus ClusteringVladimir Kiselev		Vladimir Kiselevsoftware28 Apr 20261,36892
tximportData
tximportDataMichael Love		Michael Loveexperiment5 May 20261,3300
gCrisprTools
Suite of Functions for Pooled Crispr Screen QC and AnalysisRussell Bainer		Russell Bainersoftware28 Apr 20261,17481
clusterExperiment
Compare Clusterings for Single-Cell SequencingElizabeth Purdom		Elizabeth Purdomsoftware28 Apr 20261,150147
CAGEr
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome miningCharles Plessy		Charles Plessysoftware28 Apr 20261,109174
Linnorm
Linear model and normality based normalization and transformation method (Linnorm)Shun Hang Yip		Shun Hang Yipsoftware28 Apr 20261,08862
RNAseqData.HNRNPC.bam.chr14
Aligned reads from RNAseq experiment: Transcription profiling by high throughput sequencing of HNRNPC knockdown and control HeLa cellsHervé Pagès		Hervé Pagèsexperiment5 May 20261,0690
normr
Normalization and difference calling in ChIP-seq dataJohannes Helmuth		Johannes Helmuthsoftware21 May 20261,06483
LOLA
Locus overlap analysis for enrichment of genomic rangesNathan Sheffield		Nathan Sheffieldsoftware28 Apr 20261,03924
CexoR
An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicatesPedro Madrigal		Pedro Madrigalsoftware28 Apr 20261,027101
TRONCO
TRONCO, an R package for TRanslational ONCOlogyLuca De Sano		Luca De Sanosoftware28 Apr 20261,02547
SIMLR
Single-cell Interpretation via Multi-kernel LeaRning (SIMLR)Luca De Sano		Luca De Sanosoftware28 Apr 20261,01014
chipenrich
Gene Set Enrichment For ChIP-seq Peak DataKai Wang		Kai Wangsoftware28 Apr 2026997158