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Topic: SingleCell or Classification or RNASeq

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Release: Release 3.0 (2014)

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147 packages on Bioconductor tagged SingleCell or Classification or RNASeq, most distinct IPs first

SingleCell, Classification and RNASeq 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
DESeq2
Differential gene expression analysis based on the negative binomial distributionMichael Love		Michael Lovesoftware28 Apr 202632,07254
GenomicAlignments
Representation and manipulation of short genomic alignmentsHervé Pagès		Hervé Pagèssoftware28 Apr 202627,00641
GSVA
Gene Set Variation Analysis for Microarray and RNA-Seq DataRobert Castelo		Robert Castelosoftware25 Oct 202612,75897
sva
Surrogate Variable AnalysisJeffrey T. Leek		Jeffrey T. Leeksoftware5 May 202610,80468
phyloseq
Handling and analysis of high-throughput microbiome census dataPaul J. McMurdie		Paul J. McMurdiesoftware28 Apr 20268,37966
DirichletMultinomial
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome DataMartin Morgan		Martin Morgansoftware28 Sep 20266,4909
pathview
a tool set for pathway based data integration and visualizationWeijun Luo		Weijun Luosoftware28 Apr 20265,70650
monocle
Clustering, differential expression, and trajectory analysis for single- cell RNA-SeqCole Trapnell		Cole Trapnellsoftware28 Apr 20264,48574
interactiveDisplayBase
Base package for enabling powerful shiny web displays of Bioconductor objects		no date on record2,988
Rsubread
Mapping, quantification and variant analysis of sequencing dataWei Shi		Wei Shisoftware28 Apr 20262,9518
metagenomeSeq
Statistical analysis for sparse high-throughput sequencingJoseph N. Paulson		Joseph N. Paulsonsoftware28 Apr 20262,92432
DEXSeq
Inference of differential exon usage in RNA-SeqHugo Gruson		Hugo Grusonsoftware28 Apr 20262,837107
EDASeq
Exploratory Data Analysis and Normalization for RNA-SeqDavide Risso		Davide Rissosoftware28 Apr 20262,602111
ALDEx2
Analysis Of Differential Abundance Taking Sample and Scale Variation Into AccountGreg Gloor		Greg Gloorsoftware28 Apr 20262,53356
systemPipeR
systemPipeR: A Multipurpose Workflow Management System for Reproducible Data AnalysisThomas Girke		Thomas Girkesoftware28 Apr 20262,50694
goseq
Gene Ontology analyser for RNA-seq and other length biased dataFederico Marini		Federico Marinisoftware28 Apr 20262,404104
gage
Generally Applicable Gene-set Enrichment for Pathway AnalysisWeijun Luo		Weijun Luosoftware28 Apr 20261,92944
fastseg
fastseg - a fast segmentation algorithmAlexander Blume		Alexander Blumesoftware28 Apr 20261,88413
ballgown
Flexible, isoform-level differential expression analysisJack Fu		Jack Fusoftware4 Nov 20251,84487
RUVSeq
Remove Unwanted Variation from RNA-Seq DataDavide Risso		Davide Rissosoftware28 Apr 20261,752116
DSS
Dispersion shrinkage for sequencing dataHao Wu		Hao Wusoftware28 Apr 20261,70291
pRoloc
A unifying bioinformatics framework for spatial proteomicsLisa Breckels		Lisa Breckelssoftware28 Apr 20261,689230
ReportingTools
Tools for making reports in various formatsJason A. Hackney		Jason A. Hackneysoftware28 Apr 20261,637157
MLInterfaces
Uniform interfaces to R machine learning procedures for data in Bioconductor containersVincent Carey		Vincent Careysoftware28 Apr 20261,628120
genefu
Computation of Gene Expression-Based Signatures in Breast CancerBenjamin Haibe-Kains		Benjamin Haibe-Kainssoftware28 Apr 20261,619116
QuasR
Quantify and Annotate Short Reads in RMichael Stadler		Michael Stadlersoftware28 Apr 20261,551114
derfinder
Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approachLeonardo Collado-Torres		Leonardo Collado-Torressoftware28 Apr 20261,535137
qusage
qusage: Quantitative Set Analysis for Gene ExpressionChristopher Bolen		Christopher Bolensoftware28 Apr 20261,47619