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Topic: Spatial or GeneRegulation or Pathways

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Release: Release 3.3 (2016)

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133 packages on Bioconductor tagged Spatial or GeneRegulation or Pathways, most distinct IPs first

Spatial, GeneRegulation and Pathways in Topics

PackageMaintainerCategoryLatest versionDistinct IPs a monthNeeds
KEGGREST
Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)Bioconductor Package Maintainer		Bioconductor Package Maintainersoftware18 Jun 202645,88624
edgeR
Empirical Analysis of Digital Gene Expression Data in RYunshun Chen		Yunshun Chensoftware19 Oct 202632,39210
clusterProfiler
A Universal Enrichment Tool for Interpreting Omics DataGuangchuang Yu		Guangchuang Yusoftware19 Oct 202629,661138
DOSE
Disease Ontology Semantic and Enrichment analysisGuangchuang Yu		Guangchuang Yusoftware28 Apr 202628,87377
GOSemSim
GO-terms Semantic Similarity MeasuresGuangchuang Yu		Guangchuang Yusoftware30 Jun 202627,49548
annotate
Annotation for microarraysBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 202622,55744
GSEABase
Gene set enrichment data structures and methodsBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 202613,34446
GSVA
Gene Set Variation Analysis for Microarray and RNA-Seq DataRobert Castelo		Robert Castelosoftware25 Oct 202612,75897
graphite
GRAPH Interaction from pathway Topological EnvironmentGabriele Sales		Gabriele Salessoftware28 Apr 20267,01248
KEGGgraph
KEGGgraph: A graph approach to KEGG PATHWAY in R and BioconductorJitao David Zhang		Jitao David Zhangsoftware28 Apr 20266,80714
TCGAbiolinks
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC dataTiago Chedraoui Silva		Tiago Chedraoui Silvasoftware28 Apr 20266,750103
ReactomePA
Reactome Pathway AnalysisGuangchuang Yu		Guangchuang Yusoftware28 Apr 20266,720141
pathview
a tool set for pathway based data integration and visualizationWeijun Luo		Weijun Luosoftware28 Apr 20265,70650
TFBSTools
Software Package for Transcription Factor Binding Site (TFBS) AnalysisGe Tan		Ge Tansoftware28 Apr 20264,72179
topGO
Enrichment Analysis for Gene OntologyFederico Marini		Federico Marinisoftware28 Apr 20263,22848
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
globaltest
Testing Groups of Covariates/Features for Association with a Response Variable, with Applications to Gene Set TestingJelle Goeman		Jelle Goemansoftware28 Apr 20262,84250
CNEr
CNE Detection and VisualizationBoris Lenhard		Boris Lenhardsoftware28 Apr 20262,692112
DiffBind
Differential Binding Analysis of ChIP-Seq Peak DataRory Stark		Rory Starksoftware21 Jul 20262,490141
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
Category
Category AnalysisBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 20262,35557
GlobalAncova
Global test for groups of variables via model comparisonsManuela Hummel		Manuela Hummelsoftware28 Apr 20262,06270
viper
Virtual Inference of Protein-activity by Enriched Regulon analysisMariano J Alvarez		Mariano J Alvarezsoftware28 Apr 20262,06087
gage
Generally Applicable Gene-set Enrichment for Pathway AnalysisWeijun Luo		Weijun Luosoftware28 Apr 20261,92944
rGREAT
GREAT Analysis - Functional Enrichment on Genomic RegionsZuguang Gu		Zuguang Gusoftware28 Apr 20261,663123
ReportingTools
Tools for making reports in various formatsJason A. Hackney		Jason A. Hackneysoftware28 Apr 20261,637157
UniProt.ws
R Interface to UniProt Web ServicesMarcel Ramos		Marcel Ramossoftware16 Jul 20261,61262
safe
Significance Analysis of Function and ExpressionLudwig Geistlinger		Ludwig Geistlingersoftware3 May 20261,59543