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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ChIPseeker")
AuthorGuangchuang Yu <guangchuangyu@gmail.com> with contributions from Yun Yan, Herve Pages, Michael Kluge and Thomas Schwarzl.
Bioconductor views Annotation ChIPSeq MultipleComparison Software Visualization
Date of publicationNone
MaintainerGuangchuang Yu <guangchuangyu@gmail.com>
LicenseArtistic-2.0
Version1.10.3
https://guangchuangyu.github.io/ChIPseeker

View on Bioconductor

Functions

. Man page
annotatePeak Man page
as.data.frame.csAnno Man page
as.GRanges Man page
ChIPseeker Man page
ChIPseeker-package Man page
covplot Man page
csAnno-class Man page
downloadGEObedFiles Man page
downloadGSMbedFiles Man page
dropAnno Man page
enrichAnnoOverlap Man page
enrichPeakOverlap Man page
getBioRegion Man page
getGeneAnno Man page
getGenomicAnnotation Man page
getGEOgenomeVersion Man page
getGEOInfo Man page
getGEOspecies Man page
getNearestFeatureIndicesAndDistances Man page
getPromoters Man page
getSampleFiles Man page
getTagMatrix Man page
gsminfo Man page
info Man page
overlap Man page
peakHeatmap Man page
plotAnnoBar Man page
plotAnnoBar,csAnno,ANY-method Man page
plotAnnoBar,csAnno-method Man page
plotAnnoBar.data.frame Man page
plotAnnoBar,list-method Man page
plotAnnoPie Man page
plotAnnoPie.csAnno Man page
plotAnnoPie,csAnno,ANY-method Man page
plotAnnoPie,csAnno-method Man page
plotAvgProf Man page
plotAvgProf2 Man page
plotDistToTSS Man page
plotDistToTSS,csAnno,ANY-method Man page
plotDistToTSS,csAnno-method Man page
plotDistToTSS.data.frame Man page
plotDistToTSS,list-method Man page
readPeakFile Man page
seq2gene Man page
show Man page
show,csAnno,ANY-method Man page
show,csAnno-method Man page
shuffle Man page
tagHeatmap Man page
tagMatrixList Man page
ucsc_release Man page
upsetplot Man page
upsetplot,csAnno-method Man page
vennpie Man page
vennpie,csAnno-method Man page
vennplot Man page
vennplot.peakfile Man page

Files

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

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