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Topic: Spatial or GeneRegulation

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Release: Release 3.12 (2020)

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

Spatial and GeneRegulation in Topics

PackageMaintainerCategoryLatest versionDistinct IPs a monthNeeds
SpatialExperiment
S4 Class for Spatially Resolved -omics DataDario Righelli		Dario Righellisoftware28 Apr 202610,71864
TCGAbiolinks
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC dataTiago Chedraoui Silva		Tiago Chedraoui Silvasoftware28 Apr 20266,750103
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
chromVAR
Chromatin Variation Across RegionsAlicia Schep		Alicia Schepsoftware11 May 20262,255134
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
RcisTarget
RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regionsGert Hulselmans		Gert Hulselmanssoftwareno date on record1,724
qpgraph
Estimation of Genetic and Molecular Regulatory Networks from High-Throughput Genomics DataRobert Castelo		Robert Castelosoftware28 Apr 20261,49581
GUIDEseq
GUIDE-seq and PEtag-seq analysis pipelineLihua Julie Zhu		Lihua Julie Zhusoftware28 Apr 20261,256179
INSPEcT
Modeling RNA synthesis, processing and degradation with RNA-seq dataStefano de Pretis		Stefano de Pretissoftware28 Apr 20261,213123
ATACseqQC
ATAC-seq Quality ControlJianhong Ou		Jianhong Ousoftware16 Jul 20261,150172
SPONGE
Sparse Partial Correlations On Gene ExpressionMarkus List		Markus Listsoftware11 Jun 20261,143187
BCRANK
Predicting binding site consensus from ranked DNA sequencesAdam Ameur		Adam Ameursoftware28 Apr 20261,13815
NADfinder
Call wide peaks for sequencing dataJianhong Ou		Jianhong Ousoftware28 Apr 20261,122225
rTRM
Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction NetworksDiego Diez		Diego Diezsoftware28 Apr 20261,11747
TFEA.ChIP
TFEA.ChIP, a Tool Kit for Transcription Factor EnrichmentYosra Berrouayel		Yosra Berrouayelsoftware28 Apr 20261,105106
GDCRNATools
GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDCRuidong Li		Ruidong Lisoftware28 Apr 20261,097235
pandaR
PANDA AlgorithmJoseph N. Paulson		Joseph N. Paulsonsoftware28 Apr 20261,09337
cicero
Predict cis-co-accessibility from single-cell chromatin accessibility dataHannah Pliner		Hannah Plinersoftware28 Apr 20261,077179
CAGEfightR
Analysis of Cap Analysis of Gene Expression (CAGE) data using BioconductorMalte Thodberg		Malte Thodbergsoftware28 Apr 20261,053158
MoonlightR
Identify oncogenes and tumor suppressor genes from omics dataMatteo Tiberti		Matteo Tibertisoftware28 Apr 20261,048186
LOLA
Locus overlap analysis for enrichment of genomic rangesNathan Sheffield		Nathan Sheffieldsoftware28 Apr 20261,03924
pqsfinder
Identification of potential quadruplex forming sequencesJiri Hon		Jiri Honsoftware28 Apr 20261,02818
RTN
RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulonsMauro Castro		Mauro Castrosoftware28 Apr 20261,023142
triplex
Search and visualize intramolecular triplex-forming sequences in DNAJiri Hon		Jiri Honsoftware28 Apr 20261,02217