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Topic: ChIPSeq or MicroarrayData

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Release: Release 2.10 (2012)

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30 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
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
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
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
ChIPsim
Simulation of ChIP-seq experimentsPeter Humburg		Peter Humburgsoftware28 Apr 202698654
CSAR
Statistical tools for the analysis of ChIP-seq dataJose M Muino		Jose M Muinosoftware28 Apr 202690611
DESeq
Differential gene expression analysis based on the negative binomial distribution		no date on record818
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
iASeq
iASeq: integrating multiple sequencing datasets for detecting allele-specific eventsYingying Wei		Yingying Weisoftware28 Apr 20266002
FlowSorted.Blood.450k
Illumina HumanMethylation data on sorted blood cell populationsAndrew E Jaffe		Andrew E Jaffeexperiment5 May 2026558144
MotIV
Motif Identification and Validation		no date on record396
davidTiling
Data and analysis scripts for David, Huber et al. yeast tiling array paperWolfgang Huber		Wolfgang Huberexperiment5 May 202638476
BayesPeak
Bayesian Analysis of ChIP-seq Data		no date on record339
Hiiragi2013
Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineagesWolfgang Huber		Wolfgang Huberexperiment23 Jun 202633867
pd.atdschip.tiling
Platform Design Info for Affymetrix Atdschip_tilingKristof De Beuf		Kristof De Beufexperiment5 May 202631953
NarrowPeaks
Shape-based Analysis of Variation in ChIP-seq using Functional PCA		no date on record306
ConnectivityMap
Functional connections between drugs, genes and diseases as revealed by common gene-expression changesPaul Shannon		Paul Shannonexperiment5 May 20262810
mammaPrintData
RGLists from the Glas and Buyse breast cancer studiesLuigi Marchionni		Luigi Marchionniexperiment5 May 20262690
curatedBreastData
Curated breast cancer gene expression data with survival and treatment informationLevi Waldron		Levi Waldronexperiment23 Jul 202626877
FlowSorted.DLPFC.450k
Illumina HumanMethylation data on sorted frontal cortex cell populationsAndrew E Jaffe		Andrew E Jaffeexperiment5 May 2026258144
FlowSorted.CordBloodNorway.450k
Illumina HumanMethylation data on sorted cord blood cell populationskristina gervin		kristina gervinexperiment5 May 2026243144
ccdata
Data for Combination Connectivity Mapping (ccmap) PackageAlex Pickering		Alex Pickeringexperiment5 May 20262330
FlowSorted.CordBlood.450k
Illumina 450k data on sorted cord blood cellsShan V. Andrews		Shan V. Andrewsexperiment5 May 2026221144
SVM2CRMdata
An example dataset for use with the SVM2CRM packageGuidantonio Malagoli Tagliazucchi		Guidantonio Malagoli Tagliazucchiexperiment5 May 20261870