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Topic: Spatial or GeneRegulation

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Release: Release 3.3 (2016)

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

Spatial and GeneRegulation in Topics

PackageMaintainerCategoryLatest versionDistinct IPs a monthNeeds
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
DiffBind
Differential Binding Analysis of ChIP-Seq Peak DataRory Stark		Rory Starksoftware21 Jul 20262,490141
viper
Virtual Inference of Protein-activity by Enriched Regulon analysisMariano J Alvarez		Mariano J Alvarezsoftware28 Apr 20262,06087
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
BCRANK
Predicting binding site consensus from ranked DNA sequencesAdam Ameur		Adam Ameursoftware28 Apr 20261,13815
rTRM
Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction NetworksDiego Diez		Diego Diezsoftware28 Apr 20261,11747
pandaR
PANDA AlgorithmJoseph N. Paulson		Joseph N. Paulsonsoftware28 Apr 20261,09337
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
tigre
Transcription factor Inference through Gaussian process Reconstruction of ExpressionAntti Honkela		Antti Honkelasoftware28 Apr 20261,01350
MethylMix
MethylMix: Identifying methylation driven cancer genesOlivier Gevaert		Olivier Gevaertsoftware28 Apr 202699540
tRanslatome
Comparison between multiple levels of gene expressionToma Tebaldi		Toma Tebaldisoftware28 Apr 2026956110
CRISPRseek
Design of guide RNAs in CRISPR genome-editing systemsLihua Julie Zhu		Lihua Julie Zhusoftware28 Apr 2026952141
GSRI
Gene Set Regulation IndexJulian Gehring		Julian Gehringsoftware28 Apr 202693664
IVAS
Identification of genetic Variants affecting Alternative SplicingSeonggyun Han		Seonggyun Hansoftware28 Apr 2026898112
blima
Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) levelVojtěch Kulvait		Vojtěch Kulvaitsoftware28 Apr 202686866
SELEX
Functions for analyzing SELEX-seq dataHarmen J. Bussemaker		Harmen J. Bussemakersoftware28 Apr 202686216
ELMER
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer MethylomesTiago Chedraoui Silva		Tiago Chedraoui Silvasoftware4 Feb 2026853220
MatrixRider
Obtain total affinity and occupancies for binding site matrices on a given sequenceElena Grassi		Elena Grassisoftware28 Apr 202683480
rTRMui
A shiny user interface for rTRMDiego Diez		Diego Diezsoftware28 Apr 2026813101
GSReg
Gene Set Regulation (GS-Reg)Bahman Afsari		Bahman Afsarisoftware28 Apr 202680583
diggit
Inference of Genetic Variants Driving Cellular PhenotypesMariano J Alvarez		Mariano J Alvarezsoftware28 Apr 202672596
BasicSTARRseq
Basic peak calling on STARR-seq dataAnnika Buerger		Annika Buergersoftware28 Apr 202671242