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Topic: SingleCell or Coverage or GeneExpression

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Release: Release 2.11 (2012)

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91 packages on Bioconductor tagged SingleCell or Coverage or GeneExpression, most distinct IPs first

SingleCell, Coverage and GeneExpression in Topics

PackageMaintainerCategoryLatest versionDistinct IPs a monthNeeds
GenomicRanges
Representation and manipulation of genomic intervalsHervé Pagès		Hervé Pagèssoftware28 Apr 202656,97410
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
Rsamtools
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file importBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 202630,33728
GSEABase
Gene set enrichment data structures and methodsBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 202613,34446
siggenes
Multiple Testing using SAM and Efron's Empirical Bayes ApproachesHolger Schwender		Holger Schwendersoftware28 Apr 20264,90117
oligo
Preprocessing tools for oligonucleotide arraysBenilton Carvalho		Benilton Carvalhosoftware28 Apr 20264,08752
topGO
Enrichment Analysis for Gene OntologyFederico Marini		Federico Marinisoftware28 Apr 20263,22848
Rsubread
Mapping, quantification and variant analysis of sequencing dataWei Shi		Wei Shisoftware28 Apr 20262,9518
DEXSeq
Inference of differential exon usage in RNA-SeqHugo Gruson		Hugo Grusonsoftware28 Apr 20262,837107
GOstats
Tools for manipulating GO and microarraysBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 20262,43763
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
gage
Generally Applicable Gene-set Enrichment for Pathway AnalysisWeijun Luo		Weijun Luosoftware28 Apr 20261,92944
DSS
Dispersion shrinkage for sequencing dataHao Wu		Hao Wusoftware28 Apr 20261,70291
chipseq
chipseq: A package for analyzing chipseq dataBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 20261,62654
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
qpgraph
Estimation of Genetic and Molecular Regulatory Networks from High-Throughput Genomics DataRobert Castelo		Robert Castelosoftware28 Apr 20261,49581
affycoretools
Functions useful for those doing repetitive analyses with Affymetrix GeneChipsJames W. MacDonald		James W. MacDonaldsoftware28 Apr 20261,459171
baySeq
Empirical Bayesian analysis of patterns of differential expression in count dataSamuel Granjeaud		Samuel Granjeaudsoftware28 Apr 20261,36420
puma
Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)Xuejun Liu		Xuejun Liusoftware28 Apr 20261,29655
made4
Multivariate analysis of microarray data using ADE4Aedin Culhane		Aedin Culhanesoftware28 Apr 20261,27938
BioNet
Routines for the functional analysis of biological networksMarcus Dittrich		Marcus Dittrichsoftware28 Apr 20261,26250
GeneMeta
MetaAnalysis for High Throughput ExperimentsBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 20261,23853
attract
Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor LandscapeSamuel Zimmerman		Samuel Zimmermansoftware28 Apr 20261,23769
affylmGUI
GUI for limma Package with Affymetrix MicroarraysGordon Smyth		Gordon Smythsoftware28 Apr 20261,19455
MLP
Mean Log P AnalysisTobias Verbeke		Tobias Verbekesoftware28 Apr 20261,19147
limmaGUI
GUI for limma Package With Two Color MicroarraysGordon Smyth		Gordon Smythsoftware28 Apr 20261,16511
nucleR
Nucleosome positioning package for RAlba Sala		Alba Salasoftware28 Apr 20261,14576