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Topic: ChIPSeq

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Release: Release 3.7 (2018)

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88 packages on Bioconductor, most distinct IPs first

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
ChIPseeker
ChIPseeker for ChIP peak Annotation, Comparison, and VisualizationGuangchuang Yu		Guangchuang Yusoftware28 Apr 20263,962158
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
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
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
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
ChIPQC
Quality metrics for ChIPseq dataTom Carroll		Tom Carrollsoftware19 May 20261,221159
TCseq
Time course sequencing data analysisMengjun Wu		Mengjun Wusoftware28 Apr 20261,18172
nucleR
Nucleosome positioning package for RAlba Sala		Alba Salasoftware28 Apr 20261,14576
TFEA.ChIP
TFEA.ChIP, a Tool Kit for Transcription Factor EnrichmentYosra Berrouayel		Yosra Berrouayelsoftware28 Apr 20261,105106
recoup
An R package for the creation of complex genomic profile plotsPanagiotis Moulos		Panagiotis Moulossoftware28 Apr 20261,098119
MEDIPS
DNA IP-seq data analysisLukas Chavez		Lukas Chavezsoftware28 Apr 20261,093102
Linnorm
Linear model and normality based normalization and transformation method (Linnorm)Shun Hang Yip		Shun Hang Yipsoftware28 Apr 20261,08862
normr
Normalization and difference calling in ChIP-seq dataJohannes Helmuth		Johannes Helmuthsoftware21 May 20261,06483
ChIPseqR
Identifying Protein Binding Sites in High-Throughput Sequencing DataPeter Humburg		Peter Humburgsoftware28 Apr 20261,06262
gcapc
GC Aware Peak CallerMingxiang Teng		Mingxiang Tengsoftware28 Apr 20261,04860
LOLA
Locus overlap analysis for enrichment of genomic rangesNathan Sheffield		Nathan Sheffieldsoftware28 Apr 20261,03924
CexoR
An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicatesPedro Madrigal		Pedro Madrigalsoftware28 Apr 20261,027101
chipenrich
Gene Set Enrichment For ChIP-seq Peak DataKai Wang		Kai Wangsoftware28 Apr 2026997158
ChIPsim
Simulation of ChIP-seq experimentsPeter Humburg		Peter Humburgsoftware28 Apr 202698654