Files in YuLab-SMU/ChIPseeker
ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
.Rbuildignore
.github/issue_template.md
.gitignore
.travis.yml
CONDUCT.md
DESCRIPTION
GEODATA
Makefile
NAMESPACE
NEWS
NEWS.md
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/subset.R
R/tagMatrix.R
R/upsetplot.R
R/utilities.R
R/vennpie.R
R/vennplot.R
R/zzz.R
README.Rmd
README.md
appveyor.yml
data/gsminfo.rda
data/tagMatrixList.rda
data/ucsc_release.rda
inst/CITATION
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
inst/test-plot/test-plotPeakProf.R
inst/test-plot/test-plotTagMatrix.R
man/ChIPseeker-package.Rd
man/annotatePeak.Rd
man/as.GRanges.Rd
man/as.data.frame.csAnno.Rd
man/check_upstream_and_downstream.Rd
man/combine_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/getAnnoStat.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/getTagMatrix.binning.internal.Rd
man/getTagMatrix.internal.Rd
man/getTagMatrix2.Rd
man/getTagMatrix2.binning.internal.Rd
man/getTagMatrix2.internal.Rd
man/info.Rd
man/makeBioRegionFromGranges.Rd
man/overlap.Rd
man/peakHeatmap.Rd
man/peakHeatmap_multiple_Sets.Rd
man/peak_Profile_Heatmap.Rd
man/plotAnnoBar-methods.Rd
man/plotAnnoBar.Rd
man/plotAnnoPie-methods.Rd
man/plotAnnoPie.Rd
man/plotAvgProf.Rd
man/plotAvgProf.binning.Rd
man/plotAvgProf2.Rd
man/plotDistToTSS-methods.Rd
man/plotDistToTSS.data.frame.Rd
man/plotMultiProf.Rd
man/plotMultiProf.binning.Rd
man/plotMultiProf.binning.internal.Rd
man/plotMultiProf.normal.Rd
man/plotMultiProf.normal.internal.Rd
man/plotPeakProf.Rd
man/plotPeakProf2.Rd
man/plotPeakProf_MultiWindows.Rd
man/readPeakFile.Rd
man/reexports.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/testthat.R
tests/testthat/test-bed.R
tests/testthat/test-getTagMatrix.R
tests/testthat/test-txdb.R
vignettes/ChIPseeker.Rmd
vignettes/ChIPseeker.bib
vignettes/figures/chrCoverage.png
vignettes/figures/plotAvgProf_boot.png
vignettes/figures/plotAvgProf_boot_list.png
vignettes/figures/plotPeakProf2_body_extend.png
vignettes/figures/plotPeakProf_body_boot_list_.png
vignettes/figures/upset.png
vignettes/figures/upset_vennpie.png
