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Topic: Spatial or GeneRegulation or GraphAndNetwork

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Release: Release 3.12 (2020)

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223 packages on Bioconductor tagged Spatial or GeneRegulation or GraphAndNetwork, most distinct IPs first

Spatial, GeneRegulation and GraphAndNetwork in Topics

PackageMaintainerCategoryLatest versionDistinct IPs a monthNeeds
graph
graph: A package to handle graph data structuresBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 202625,6557
GSEABase
Gene set enrichment data structures and methodsBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 202613,34446
Rgraphviz
Provides plotting capabilities for R graph objectsKasper Daniel Hansen		Kasper Daniel Hansensoftware28 Apr 202611,26310
SpatialExperiment
S4 Class for Spatially Resolved -omics DataDario Righelli		Dario Righellisoftware28 Apr 202610,71864
RBGL
An interface to the BOOST graph libraryBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 202610,6989
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
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
Rsubread
Mapping, quantification and variant analysis of sequencing dataWei Shi		Wei Shisoftware28 Apr 20262,9518
CNEr
CNE Detection and VisualizationBoris Lenhard		Boris Lenhardsoftware28 Apr 20262,692112
OmnipathR
OmniPath web service client and moreDenes Turei		Denes Tureisoftware30 Apr 20262,68589
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
chromVAR
Chromatin Variation Across RegionsAlicia Schep		Alicia Schepsoftware11 May 20262,255134
GENIE3
GEne Network Inference with Ensemble of treesVan Anh Huynh-Thu		Van Anh Huynh-Thusoftware28 Apr 20262,25326
universalmotif
Import, Modify, and Export Motifs with RBenjamin Jean-Marie Tremblay		Benjamin Jean-Marie Tremblaysoftware3 May 20262,13339
viper
Virtual Inference of Protein-activity by Enriched Regulon analysisMariano J Alvarez		Mariano J Alvarezsoftware28 Apr 20262,06087
progeny
Pathway RespOnsive GENes for activity inference from gene expressionAurélien Dugourd		Aurélien Dugourdsoftware28 Apr 20262,01258
SPIA
Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbationsAdi Laurentiu Tarca		Adi Laurentiu Tarcasoftware28 Apr 20261,83915
RCy3
Functions to Access and Control CytoscapeJing Chen		Jing Chensoftware28 Apr 20261,82249
RcisTarget
RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regionsGert Hulselmans		Gert Hulselmanssoftwareno date on record1,724
minet
Mutual Information NETworksPatrick E. Meyer		Patrick E. Meyersoftware28 Apr 20261,5431
qpgraph
Estimation of Genetic and Molecular Regulatory Networks from High-Throughput Genomics DataRobert Castelo		Robert Castelosoftware28 Apr 20261,49581
EnrichmentBrowser
Seamless navigation through combined results of set-based and network-based enrichment analysisLudwig Geistlinger		Ludwig Geistlingersoftware28 Apr 20261,43292
RedeR
Interactive visualization and manipulation of nested networksMauro Castro		Mauro Castrosoftware14 Jul 20261,31723
BioNet
Routines for the functional analysis of biological networksMarcus Dittrich		Marcus Dittrichsoftware28 Apr 20261,26250
GUIDEseq
GUIDE-seq and PEtag-seq analysis pipelineLihua Julie Zhu		Lihua Julie Zhusoftware28 Apr 20261,256179
GeneNetworkBuilder
GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-seq data and Gene Expression DataJianhong Ou		Jianhong Ousoftware28 Apr 20261,21669