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Topic: SingleCell or Transcriptomics

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Release: Release 3.8 (2018)

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108 packages on Bioconductor tagged SingleCell or Transcriptomics, most distinct IPs first

SingleCell and Transcriptomics 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
SingleCellExperiment
S4 Classes for Single Cell DataDavide Risso		Davide Rissosoftware28 Apr 202624,48325
HDF5Array
HDF5 datasets as array-like objects in RHervé Pagès		Hervé Pagèssoftware28 Apr 202620,53728
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
tximport
Import and summarize transcript-level estimates for transcript- and gene-level analysisMichael Love		Michael Lovesoftware28 Apr 20265,8043
slingshot
Tools for ordering single-cell sequencingKelly Street		Kelly Streetsoftware28 Apr 20264,68438
AUCell
AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)Gert Hulselmans		Gert Hulselmanssoftware29 Apr 20264,610115
DropletUtils
Utilities for Handling Single-Cell Droplet DataJonathan Griffiths		Jonathan Griffithssoftware27 Sep 20264,10759
MAST
Model-based Analysis of Single Cell TranscriptomicsAndrew McDavid		Andrew McDavidsoftware28 Apr 20263,74056
topGO
Enrichment Analysis for Gene OntologyFederico Marini		Federico Marinisoftware28 Apr 20263,22848
variancePartition
Quantify and interpret drivers of variation in multilevel gene expression experimentsGabriel E. Hoffman		Gabriel E. Hoffmansoftware28 Apr 20263,21199
ropls
PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics dataEtienne A. Thevenot		Etienne A. Thevenotsoftware28 Apr 20262,96997
Rsubread
Mapping, quantification and variant analysis of sequencing dataWei Shi		Wei Shisoftware28 Apr 20262,9518
ALDEx2
Analysis Of Differential Abundance Taking Sample and Scale Variation Into AccountGreg Gloor		Greg Gloorsoftware28 Apr 20262,53356
tximeta
Transcript Quantification Import with Automatic MetadataMichael Love		Michael Lovesoftware26 Oct 20262,485108
chromVAR
Chromatin Variation Across RegionsAlicia Schep		Alicia Schepsoftware11 May 20262,255134
RcisTarget
RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regionsGert Hulselmans		Gert Hulselmanssoftwareno date on record1,724
zinbwave
Zero-Inflated Negative Binomial Model for RNA-Seq DataDavide Risso		Davide Rissosoftware28 Apr 20261,56974
splatter
Simple Simulation of Single-cell RNA Sequencing DataLuke Zappia		Luke Zappiasoftware28 Apr 20261,55361
IsoformSwitchAnalyzeR
Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq dataKristoffer Vitting-Seerup		Kristoffer Vitting-Seerupsoftware28 Apr 20261,421151
SC3
Single-Cell Consensus ClusteringVladimir Kiselev		Vladimir Kiselevsoftware28 Apr 20261,36892
made4
Multivariate analysis of microarray data using ADE4Aedin Culhane		Aedin Culhanesoftware28 Apr 20261,27938
scmap
A tool for unsupervised projection of single cell RNA-seq dataVladimir Kiselev		Vladimir Kiselevsoftware28 Apr 20261,27062
CATALYST
Cytometry dATa anALYSis ToolsHelena L. Crowell		Helena L. Crowellsoftware28 Apr 20261,265176
iSEE
Interactive SummarizedExperiment ExplorerKevin Rue-Albrecht		Kevin Rue-Albrechtsoftware28 Apr 20261,237109
singleCellTK
Comprehensive and Interactive Analysis of Single Cell RNA-Seq DataJoshua David Campbell		Joshua David Campbellsoftware29 Apr 20261,218392
BASiCS
Bayesian Analysis of Single-Cell Sequencing dataCatalina Vallejos		Catalina Vallejossoftware29 Apr 20261,206129
diffcyt
Differential discovery in high-dimensional cytometry via high-resolution clusteringLukas M. Weber		Lukas M. Webersoftware16 Jul 20261,152146