Package: ChIPseeker 1.41.0

Guangchuang Yu

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.

Authors:Guangchuang Yu [aut, cre], Ming Li [ctb], Qianwen Wang [ctb], Yun Yan [ctb], Hervé Pagès [ctb], Michael Kluge [ctb], Thomas Schwarzl [ctb], Zhougeng Xu [ctb]

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ChIPseeker.pdf |ChIPseeker.html✨
ChIPseeker/json (API)
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Bug tracker:https://github.com/yulab-smu/chipseeker/issues

On BioConductor:ChIPseeker-1.41.0(bioc 3.20)ChIPseeker-1.40.0(bioc 3.19)

bioconductor-package

42 exports 2.46 score 143 dependencies 5 dependents 161 mentions

Last updated 2 months agofrom:dc9c243370

Exports:.annotatePeakas.GRangescombine_csAnnocovplotdownloadGEObedFilesdownloadGSMbedFilesdropAnnoenrichAnnoOverlapenrichPeakOverlapgetAnnoStatgetBioRegiongetGEOgenomeVersiongetGEOInfogetGEOspeciesgetPromotersgetSampleFilesgetTagMatrixGRangesListmakeBioRegionFromGrangesoverlappeak_Profile_HeatmappeakHeatmappeakHeatmap_multiple_SetsplotAnnoBarplotAnnoPieplotAnnoPie.csAnnoplotAvgProfplotAvgProf2plotDistToTSSplotPeakProfplotPeakProf2readPeakFilerelseq2geneshowshuffletagHeatmapupsetplotvennpievennplotvennplot.peakfile

Dependencies:abindAnnotationDbiapeaplotaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbootcachemcaToolsclicodetoolscolorspacecowplotcpp11crayoncurldata.tableDBIDelayedArraydigestDOSEdplyrenrichplotfansifarverfastmapfastmatchfgseaformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggforceggfunggnewscaleggplot2ggplotifyggraphggrepelggtreeglueGO.dbGOSemSimgplotsgraphlayoutsgridExtragridGraphicsgtablegtoolsHDO.dbhttrigraphIRangesisobandjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpatchworkpillarpkgconfigplogrplotrixplyrpngpolyclippurrrqvalueR6RColorBrewerRcppRcppArmadilloRcppEigenRCurlreshape2restfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalesscatterpieshadowtextsnowSparseArraystringistringrSummarizedExperimentsyssystemfontstibbletidygraphtidyrtidyselecttidytreetreeiotweenrTxDb.Hsapiens.UCSC.hg19.knownGeneUCSC.utilsutf8vctrsviridisviridisLitewithrXMLXVectoryamlyulab.utilszlibbioc