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Topic: VariantAnnotation or Bayesian or GeneSetEnrichment

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Release: Release 3.0 (2014)

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72 packages on Bioconductor tagged VariantAnnotation or Bayesian or GeneSetEnrichment, most distinct IPs first

VariantAnnotation, Bayesian and GeneSetEnrichment in Topics

PackageMaintainerCategoryLatest versionDistinct IPs a monthNeeds
limma
Linear Models for Microarray and Omics DataGordon Smyth		Gordon Smythsoftware10 Aug 202644,6566
DESeq2
Differential gene expression analysis based on the negative binomial distributionMichael Love		Michael Lovesoftware28 Apr 202631,84554
edgeR
Empirical Analysis of Digital Gene Expression Data in RYunshun Chen		Yunshun Chensoftware19 Oct 202631,06510
clusterProfiler
A Universal Enrichment Tool for Interpreting Omics DataGuangchuang Yu		Guangchuang Yusoftware19 Oct 202628,951138
DOSE
Disease Ontology Semantic and Enrichment analysisGuangchuang Yu		Guangchuang Yusoftware28 Apr 202628,33577
GSEABase
Gene set enrichment data structures and methodsBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 202613,10746
GSVA
Gene Set Variation Analysis for Microarray and RNA-Seq DataRobert Castelo		Robert Castelosoftware25 Oct 202612,44697
VariantAnnotation
Annotation of Genetic VariantsBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 20269,77176
pcaMethods
A collection of PCA methodsHenning Redestig		Henning Redestigsoftware28 Apr 20267,21410
ReactomePA
Reactome Pathway AnalysisGuangchuang Yu		Guangchuang Yusoftware28 Apr 20266,534141
pathview
a tool set for pathway based data integration and visualizationWeijun Luo		Weijun Luosoftware28 Apr 20265,66750
topGO
Enrichment Analysis for Gene OntologyFederico Marini		Federico Marinisoftware28 Apr 20263,05548
Rsubread
Mapping, quantification and variant analysis of sequencing dataWei Shi		Wei Shisoftware28 Apr 20262,7228
ALDEx2
Analysis Of Differential Abundance Taking Sample and Scale Variation Into AccountGreg Gloor		Greg Gloorsoftware28 Apr 20262,31156
GOstats
Tools for manipulating GO and microarraysBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 20262,23663
systemPipeR
systemPipeR: A Multipurpose Workflow Management System for Reproducible Data AnalysisThomas Girke		Thomas Girkesoftware28 Apr 20262,23594
Category
Category AnalysisBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 20262,19457
goseq
Gene Ontology analyser for RNA-seq and other length biased dataFederico Marini		Federico Marinisoftware28 Apr 20262,176104
missMethyl
Analysing Illumina HumanMethylation BeadChip DataBelinda Phipson		Belinda Phipsonsoftware12 May 20261,816169
gage
Generally Applicable Gene-set Enrichment for Pathway AnalysisWeijun Luo		Weijun Luosoftware28 Apr 20261,71344
ReportingTools
Tools for making reports in various formatsJason A. Hackney		Jason A. Hackneysoftware28 Apr 20261,439157
safe
Significance Analysis of Function and ExpressionLudwig Geistlinger		Ludwig Geistlingersoftware3 May 20261,40143
piano
Platform for integrative analysis of omics dataLeif Varemo Wigge		Leif Varemo Wiggesoftware28 Apr 20261,31994
EnrichmentBrowser
Seamless navigation through combined results of set-based and network-based enrichment analysisLudwig Geistlinger		Ludwig Geistlingersoftware28 Apr 20261,23692
qusage
qusage: Quantitative Set Analysis for Gene ExpressionChristopher Bolen		Christopher Bolensoftware28 Apr 20261,18019
baySeq
Empirical Bayesian analysis of patterns of differential expression in count dataSamuel Granjeaud		Samuel Granjeaudsoftware28 Apr 20261,16820
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 20261,03355
CAFE
Chromosmal Aberrations Finder in Expression dataSander Bollen		Sander Bollensoftware28 Apr 2026985141
attract
Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor LandscapeSamuel Zimmerman		Samuel Zimmermansoftware28 Apr 202696869
affylmGUI
GUI for limma Package with Affymetrix MicroarraysGordon Smyth		Gordon Smythsoftware28 Apr 202696755