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Topic: VariantAnnotation or Bayesian or GeneSetEnrichment

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289 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
enrichplot
Visualization of Functional Enrichment ResultGuangchuang Yu		Guangchuang Yusoftware28 Sep 202629,750128
clusterProfiler
A Universal Enrichment Tool for Interpreting Omics DataGuangchuang Yu		Guangchuang Yusoftware19 Oct 202628,951138
fgsea
Fast Gene Set Enrichment AnalysisAlexey Sergushichev		Alexey Sergushichevsoftware28 Apr 202628,70238
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
apeglm
Approximate posterior estimation for GLM coefficientsAnqi Zhu		Anqi Zhusoftware28 Apr 20267,16136
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
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 20264,433115
UCell
Rank-based signature enrichment analysis for single-cell dataMassimo Andreatta		Massimo Andreattasoftware28 Apr 20263,53941
MAST
Model-based Analysis of Single Cell TranscriptomicsAndrew McDavid		Andrew McDavidsoftware28 Apr 20263,51356
maftools
Summarize, Analyze and Visualize MAF FilesAnand Mayakonda		Anand Mayakondasoftware28 Apr 20263,41926
topGO
Enrichment Analysis for Gene OntologyFederico Marini		Federico Marinisoftware28 Apr 20263,05548
variancePartition
Quantify and interpret drivers of variation in multilevel gene expression experimentsGabriel E. Hoffman		Gabriel E. Hoffmansoftware28 Apr 20262,89599
singscore
Rank-based single-sample gene set scoring methodMalvika Kharbanda		Malvika Kharbandasoftware28 Apr 20262,759120
Rsubread
Mapping, quantification and variant analysis of sequencing dataWei Shi		Wei Shisoftware28 Apr 20262,7228
infercnv
Infer Copy Number Variation from Single-Cell RNA-Seq DataChristophe Georgescu		Christophe Georgescusoftware28 Apr 20262,517194
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
celda
CEllular Latent Dirichlet AllocationJoshua Campbell		Joshua Campbellsoftware28 Apr 20262,011127
missMethyl
Analysing Illumina HumanMethylation BeadChip DataBelinda Phipson		Belinda Phipsonsoftware12 May 20261,816169