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Topic: ChIPSeq or MicroarrayData

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Release: Release 2.14 (2014)

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124 packages on Bioconductor tagged ChIPSeq or MicroarrayData, most distinct IPs first

ChIPSeq and MicroarrayData 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
Rsubread
Mapping, quantification and variant analysis of sequencing dataWei Shi		Wei Shisoftware28 Apr 20262,9518
DiffBind
Differential Binding Analysis of ChIP-Seq Peak DataRory Stark		Rory Starksoftware21 Jul 20262,490141
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
affydata
Affymetrix Data for Demonstration PurposeRobert D Shear		Robert D Shearexperiment5 May 20261,24412
ChIPQC
Quality metrics for ChIPseq dataTom Carroll		Tom Carrollsoftware19 May 20261,221159
nucleR
Nucleosome positioning package for RAlba Sala		Alba Salasoftware28 Apr 20261,14576
MEDIPS
DNA IP-seq data analysisLukas Chavez		Lukas Chavezsoftware28 Apr 20261,093102
ChIPseqR
Identifying Protein Binding Sites in High-Throughput Sequencing DataPeter Humburg		Peter Humburgsoftware28 Apr 20261,06262
bladderbatch
Bladder gene expression data illustrating batch effectsJeffrey T. Leek		Jeffrey T. Leekexperiment5 May 20261,0497
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
epigenomix
Epigenetic and gene transcription data normalization and integration with mixture modelsHans-Ulrich Klein		Hans-Ulrich Kleinsoftware28 Apr 202696397
CSAR
Statistical tools for the analysis of ChIP-seq dataJose M Muino		Jose M Muinosoftware28 Apr 202690611
CoverageView
Coverage visualization package for RErnesto Lowy		Ernesto Lowysoftware28 Apr 202684957
DESeq
Differential gene expression analysis based on the negative binomial distribution		no date on record818
minfiData
Example data for the Illumina Methylation 450k arrayKasper Daniel Hansen		Kasper Daniel Hansenexperiment5 May 2026788146
TransView
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets		no date on record732
rGADEM
de novo motif discovery		no date on record722
iSeq
Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising ModelsQianxing Mo		Qianxing Mosoftware28 Apr 20267150
fibroEset
exprSet for Karaman et al. (2003) fibroblasts dataSylvia Merk		Sylvia Merkexperiment5 May 20267087
ChIPXpress
ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profilesGeorge Wu		George Wusoftware28 Apr 2026701103
Illumina450ProbeVariants.db
Annotation Package combining variant data from 1000 Genomes Project for Illumina HumanMethylation450 Bead Chip probesTiffany Morris		Tiffany Morrisexperiment5 May 20266900
gageData
Auxillary data for gage packageWeijun Luo		Weijun Luoexperiment5 May 20266230