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Topic: Spatial or GeneRegulation or SNP

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Release: Release 3.16 (2022)

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

Spatial, GeneRegulation and SNP in Topics

PackageMaintainerCategoryLatest versionDistinct IPs a monthNeeds
GenomicAlignments
Representation and manipulation of short genomic alignmentsHervé Pagès		Hervé Pagèssoftware28 Apr 202627,00641
BSgenome
Software infrastructure for efficient representation of full genomes and their SNPsHervé Pagès		Hervé Pagèssoftware28 Apr 202614,37557
SpatialExperiment
S4 Class for Spatially Resolved -omics DataDario Righelli		Dario Righellisoftware28 Apr 202610,71864
VariantAnnotation
Annotation of Genetic VariantsBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 20269,66476
TCGAbiolinks
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC dataTiago Chedraoui Silva		Tiago Chedraoui Silvasoftware28 Apr 20266,750103
siggenes
Multiple Testing using SAM and Efron's Empirical Bayes ApproachesHolger Schwender		Holger Schwendersoftware28 Apr 20264,90117
TFBSTools
Software Package for Transcription Factor Binding Site (TFBS) AnalysisGe Tan		Ge Tansoftware28 Apr 20264,72179
oligo
Preprocessing tools for oligonucleotide arraysBenilton Carvalho		Benilton Carvalhosoftware28 Apr 20264,08752
decoupleR
decoupleR: Ensemble of computational methods to infer biological activities from omics dataPau Badia-i-Mompel		Pau Badia-i-Mompelsoftware30 Oct 20253,63441
snpStats
SnpMatrix and XSnpMatrix classes and methodsDavid Clayton		David Claytonsoftware28 Apr 20263,48812
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
systemPipeR
systemPipeR: A Multipurpose Workflow Management System for Reproducible Data AnalysisThomas Girke		Thomas Girkesoftware28 Apr 20262,50694
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
GWASTools
Tools for Genome Wide Association StudiesStephanie M. Gogarten		Stephanie M. Gogartensoftware28 Apr 20261,63494
crlmm
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arraysBenilton S Carvalho		Benilton S Carvalhosoftware28 Apr 20261,50465
qpgraph
Estimation of Genetic and Molecular Regulatory Networks from High-Throughput Genomics DataRobert Castelo		Robert Castelosoftware28 Apr 20261,49581
sangerseqR
Tools for Sanger Sequencing Data in RJonathon Hill		Jonathon Hillsoftware28 Apr 20261,45249
GENESIS
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatednessStephanie M. Gogarten		Stephanie M. Gogartensoftware28 Apr 20261,444117
SeqVarTools
Tools for variant dataStephanie M. Gogarten		Stephanie M. Gogartensoftware12 Jul 20261,42089
GeneRegionScan
GeneRegionScanLasse Folkersen		Lasse Folkersensoftware28 Apr 20261,38918
deepSNV
Detection of subclonal SNVs in deep sequencing data.Moritz Gerstung		Moritz Gerstungsoftware28 Apr 20261,28679
GUIDEseq
GUIDE-seq and PEtag-seq analysis pipelineLihua Julie Zhu		Lihua Julie Zhusoftware28 Apr 20261,256179
VariantFiltering
Filtering of coding and non-coding genetic variantsRobert Castelo		Robert Castelosoftware28 Apr 20261,223178