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Topic: Spatial or GeneRegulation or ChIPSeq

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Release: Release 3.18 (2023)

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

Spatial, GeneRegulation and ChIPSeq in Topics

PackageMaintainerCategoryLatest versionDistinct IPs a monthNeeds
edgeR
Empirical Analysis of Digital Gene Expression Data in RYunshun Chen		Yunshun Chensoftware19 Oct 202632,39210
DESeq2
Differential gene expression analysis based on the negative binomial distributionMichael Love		Michael Lovesoftware28 Apr 202632,07254
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
ChIPseeker
ChIPseeker for ChIP peak Annotation, Comparison, and VisualizationGuangchuang Yu		Guangchuang Yusoftware28 Apr 20263,962158
decoupleR
decoupleR: Ensemble of computational methods to infer biological activities from omics dataPau Badia-i-Mompel		Pau Badia-i-Mompelsoftware30 Oct 20253,63441
regioneR
Association analysis of genomic regions based on permutation testsBernat Gel		Bernat Gelsoftware28 Apr 20262,95264
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
ALDEx2
Analysis Of Differential Abundance Taking Sample and Scale Variation Into AccountGreg Gloor		Greg Gloorsoftware28 Apr 20262,53356
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
karyoploteR
Plot customizable linear genomes displaying arbitrary dataBernat Gel		Bernat Gelsoftware28 Apr 20261,962131
GreyListChIP
Grey Lists -- Mask Artefact Regions Based on ChIP InputsMatt Eldridge		Matt Eldridgesoftware28 Apr 20261,94259
ChIPpeakAnno
Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval dataJianhong Ou		Jianhong Ousoftware10 Aug 20261,898125
motifStack
Plot stacked logos for single or multiple DNA, RNA and amino acid sequenceJianhong Ou		Jianhong Ousoftware28 Apr 20261,782111
RcisTarget
RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regionsGert Hulselmans		Gert Hulselmanssoftwareno date on record1,724
chipseq
chipseq: A package for analyzing chipseq dataBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 20261,62654
QuasR
Quantify and Annotate Short Reads in RMichael Stadler		Michael Stadlersoftware28 Apr 20261,551114
csaw
ChIP-Seq Analysis with WindowsAaron Lun		Aaron Lunsoftware28 Apr 20261,53646
derfinder
Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approachLeonardo Collado-Torres		Leonardo Collado-Torressoftware28 Apr 20261,535137
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
ChIPQC
Quality metrics for ChIPseq dataTom Carroll		Tom Carrollsoftware19 May 20261,221159