ChIPseeker: ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statstical methods for estimate the significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. Several visualization functions are implemented to summarize the coverage of the peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.

AuthorGuangchuang Yu <guangchuangyu@gmail.com> with contributions from Yun Yan, Herve Pages, Michael Kluge and Thomas Schwarzl.
Date of publicationNone
MaintainerGuangchuang Yu <guangchuangyu@gmail.com>
LicenseArtistic-2.0
Version1.10.3
https://guangchuangyu.github.io/ChIPseeker

View on Bioconductor

Files in this package

ChIPseeker/DESCRIPTION
ChIPseeker/NAMESPACE
ChIPseeker/NEWS
ChIPseeker/R
ChIPseeker/R/AllGenerics.R ChIPseeker/R/ChIPseeker-package.R ChIPseeker/R/GEO.R ChIPseeker/R/addGeneAnno.R ChIPseeker/R/annotatePeak.R ChIPseeker/R/covplot.R ChIPseeker/R/csAnno.R ChIPseeker/R/enrichOverlap.R ChIPseeker/R/getFlankingGene.R ChIPseeker/R/getGenomicAnnotation.R ChIPseeker/R/getNearestFeatureIndicesAndDistances.R ChIPseeker/R/plotAnno.R ChIPseeker/R/plotDistToTSS.R ChIPseeker/R/plotTagMatrix.R ChIPseeker/R/readPeakFile.R ChIPseeker/R/seq2gene.R ChIPseeker/R/tagMatrix.R ChIPseeker/R/upsetplot.R ChIPseeker/R/utilities.R ChIPseeker/R/vennpie.R ChIPseeker/R/vennplot.R ChIPseeker/R/zzz.R
ChIPseeker/README.md
ChIPseeker/build
ChIPseeker/build/vignette.rds
ChIPseeker/data
ChIPseeker/data/datalist
ChIPseeker/data/gsminfo.rda
ChIPseeker/data/tagMatrixList.rda
ChIPseeker/data/ucsc_release.rda
ChIPseeker/inst
ChIPseeker/inst/CITATION
ChIPseeker/inst/doc
ChIPseeker/inst/doc/ChIPseeker.R
ChIPseeker/inst/doc/ChIPseeker.Rmd
ChIPseeker/inst/doc/ChIPseeker.html
ChIPseeker/inst/extdata
ChIPseeker/inst/extdata/GEO_sample_data
ChIPseeker/inst/extdata/GEO_sample_data/GSM1174480_ARmo_0M_peaks.bed.gz
ChIPseeker/inst/extdata/GEO_sample_data/GSM1174481_ARmo_1nM_peaks.bed.gz
ChIPseeker/inst/extdata/GEO_sample_data/GSM1174482_ARmo_100nM_peaks.bed.gz
ChIPseeker/inst/extdata/GEO_sample_data/GSM1295076_CBX6_BF_ChipSeq_mergedReps_peaks.bed.gz
ChIPseeker/inst/extdata/GEO_sample_data/GSM1295077_CBX7_BF_ChipSeq_mergedReps_peaks.bed.gz
ChIPseeker/inst/extdata/processedGSM.rda
ChIPseeker/inst/extdata/sample_peaks.txt
ChIPseeker/man
ChIPseeker/man/ChIPseeker-package.Rd ChIPseeker/man/annotatePeak.Rd ChIPseeker/man/as.GRanges.Rd ChIPseeker/man/as.data.frame.csAnno.Rd ChIPseeker/man/covplot.Rd ChIPseeker/man/csAnno-class.Rd ChIPseeker/man/dotFun.Rd ChIPseeker/man/downloadGEObedFiles.Rd ChIPseeker/man/downloadGSMbedFiles.Rd ChIPseeker/man/dropAnno.Rd ChIPseeker/man/enrichAnnoOverlap.Rd ChIPseeker/man/enrichPeakOverlap.Rd ChIPseeker/man/getBioRegion.Rd ChIPseeker/man/getGEOInfo.Rd ChIPseeker/man/getGEOgenomeVersion.Rd ChIPseeker/man/getGEOspecies.Rd ChIPseeker/man/getGeneAnno.Rd ChIPseeker/man/getGenomicAnnotation.Rd ChIPseeker/man/getNearestFeatureIndicesAndDistances.Rd ChIPseeker/man/getPromoters.Rd ChIPseeker/man/getSampleFiles.Rd ChIPseeker/man/getTagMatrix.Rd ChIPseeker/man/info.Rd ChIPseeker/man/overlap.Rd ChIPseeker/man/peakHeatmap.Rd ChIPseeker/man/plotAnnoBar-methods.Rd ChIPseeker/man/plotAnnoBar.data.frame.Rd ChIPseeker/man/plotAnnoPie-methods.Rd ChIPseeker/man/plotAnnoPie.csAnno.Rd ChIPseeker/man/plotAvgProf.Rd ChIPseeker/man/plotAvgProf2.Rd ChIPseeker/man/plotDistToTSS-methods.Rd ChIPseeker/man/plotDistToTSS.data.frame.Rd ChIPseeker/man/readPeakFile.Rd ChIPseeker/man/seq2gene.Rd ChIPseeker/man/show-methods.Rd ChIPseeker/man/shuffle.Rd ChIPseeker/man/tagHeatmap.Rd ChIPseeker/man/upsetplot-methods.Rd ChIPseeker/man/vennpie-methods.Rd ChIPseeker/man/vennplot.Rd ChIPseeker/man/vennplot.peakfile.Rd
ChIPseeker/tests
ChIPseeker/tests/testthat
ChIPseeker/tests/testthat.R
ChIPseeker/tests/testthat/test-bed.R
ChIPseeker/tests/testthat/test-txdb.R
ChIPseeker/vignettes
ChIPseeker/vignettes/ChIPseeker.Rmd
ChIPseeker/vignettes/ChIPseeker.bib
ChIPseeker/vignettes/figures
ChIPseeker/vignettes/figures/chrCoverage.png
ChIPseeker/vignettes/figures/plotAvgProf_boot.png
ChIPseeker/vignettes/figures/plotAvgProf_boot_list.png
ChIPseeker/vignettes/figures/upset.png
ChIPseeker/vignettes/figures/upset_vennpie.png
ChIPseeker/vignettes/nature.csl

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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