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Topic: SingleCell or Epigenetics or DifferentialExpression

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Release: Release 3.0 (2014)

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173 packages on Bioconductor tagged SingleCell or Epigenetics or DifferentialExpression, most distinct IPs first

SingleCell, Epigenetics and DifferentialExpression 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
multtest
Resampling-based multiple hypothesis testingKatherine S. Pollard		Katherine S. Pollardsoftware28 Apr 202614,45715
pathview
a tool set for pathway based data integration and visualizationWeijun Luo		Weijun Luosoftware28 Apr 20265,70650
siggenes
Multiple Testing using SAM and Efron's Empirical Bayes ApproachesHolger Schwender		Holger Schwendersoftware28 Apr 20264,90117
monocle
Clustering, differential expression, and trajectory analysis for single- cell RNA-SeqCole Trapnell		Cole Trapnellsoftware28 Apr 20264,48574
bumphunter
Bump HunterTamilselvi Guharaj		Tamilselvi Guharajsoftware28 Apr 20264,26883
oligo
Preprocessing tools for oligonucleotide arraysBenilton Carvalho		Benilton Carvalhosoftware28 Apr 20264,08752
minfi
Analyze Illumina Infinium DNA methylation arraysKasper Daniel Hansen		Kasper Daniel Hansensoftware28 Apr 20264,041143
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
globaltest
Testing Groups of Covariates/Features for Association with a Response Variable, with Applications to Gene Set TestingJelle Goeman		Jelle Goemansoftware28 Apr 20262,84250
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
DiffBind
Differential Binding Analysis of ChIP-Seq Peak DataRory Stark		Rory Starksoftware21 Jul 20262,490141
goseq
Gene Ontology analyser for RNA-seq and other length biased dataFederico Marini		Federico Marinisoftware28 Apr 20262,404104
survcomp
Performance Assessment and Comparison for Survival AnalysisBenjamin Haibe-Kains		Benjamin Haibe-Kainssoftware28 Apr 20262,38355
ROC
utilities for ROC, with microarray focusVince Carey		Vince Careysoftware28 Apr 20262,15910
GlobalAncova
Global test for groups of variables via model comparisonsManuela Hummel		Manuela Hummelsoftware28 Apr 20262,06270
gage
Generally Applicable Gene-set Enrichment for Pathway AnalysisWeijun Luo		Weijun Luosoftware28 Apr 20261,92944
ballgown
Flexible, isoform-level differential expression analysisJack Fu		Jack Fusoftware4 Nov 20251,84487
DMRcate
Methylation array and sequencing spatial analysis methodsTim Peters		Tim Peterssoftware3 May 20261,838224
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
genefu
Computation of Gene Expression-Based Signatures in Breast CancerBenjamin Haibe-Kains		Benjamin Haibe-Kainssoftware28 Apr 20261,619116
safe
Significance Analysis of Function and ExpressionLudwig Geistlinger		Ludwig Geistlingersoftware3 May 20261,59543
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
piano
Platform for integrative analysis of omics dataLeif Varemo Wigge		Leif Varemo Wiggesoftware28 Apr 20261,50994