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

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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.

Author
Guangchuang Yu <guangchuangyu@gmail.com> with contributions from Yun Yan, Herve Pages, Michael Kluge and Thomas Schwarzl.
Date of publication
None
Maintainer
Guangchuang Yu <guangchuangyu@gmail.com>
License
Artistic-2.0
Version
1.10.2
URLs

View on Bioconductor

Man pages

annotatePeak
annotatePeak
as.data.frame.csAnno
as.data.frame.csAnno
as.GRanges
as.GRanges
ChIPseeker-package
ChIP-SEQ Annotation, Visualization and Comparison
covplot
covplot
csAnno-class
Class "csAnno" This class represents the output of ChIPseeker...
dotFun
.
downloadGEObedFiles
downloadGEObedFiles
downloadGSMbedFiles
downloadGSMbedFiles
dropAnno
dropAnno
enrichAnnoOverlap
enrichAnnoOverlap
enrichPeakOverlap
enrichPeakOverlap
getBioRegion
getBioRegion
getGeneAnno
getGeneAnno
getGenomicAnnotation
getGenomicAnnotation
getGEOgenomeVersion
getGEOgenomeVersion
getGEOInfo
getGEOInfo
getGEOspecies
getGEOspecies
getNearestFeatureIndicesAndDistances
getNearestFeatureIndicesAndDistances
getPromoters
getPromoters
getSampleFiles
getSampleFiles
getTagMatrix
getTagMatrix
info
Information Datasets
overlap
overlap
peakHeatmap
peakHeatmap
plotAnnoBar.data.frame
plotAnnoBar.data.frame
plotAnnoBar-methods
plotAnnoBar method generics
plotAnnoPie.csAnno
plotAnnoPie
plotAnnoPie-methods
plotAnnoPie method generics
plotAvgProf
plotAvgProf
plotAvgProf2
plotAvgProf
plotDistToTSS.data.frame
plotDistToTSS.data.frame
plotDistToTSS-methods
plotDistToTSS method generics
readPeakFile
readPeakFile
seq2gene
seq2gene
show-methods
show method
shuffle
shuffle
tagHeatmap
tagHeatmap
upsetplot-methods
upsetplot method
vennpie-methods
vennpie method generics
vennplot
vennplot
vennplot.peakfile
vennplot.peakfile

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