# epiSeeker: an R package for Annotation, Comparison and Visualization of multi-omics epigenetic data

## Documentation for package ‘epiSeeker’ version 1.1.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

. | .
.epiSeekerEnv | Env function for epiSeeker
annotateSeq | annotateSeq
arrange.GRanges | Arrange GRanges object
as.data.frame.csAnno | as.data.frame.csAnno
as.GRanges | as.GRanges
bin_vector | bin vector function
bmData | Constructor for bmData objects
bmData-class | bmData Class
bmData-methods | getBmMatrix methods generics
BSseq-methods | getBmMatrix methods generics
check_bin | check bin parameter method
check_extension | check upstream and downstream extension
check_windows | check windows function
combine_csAnno | combine_csAnno
create_regex_patterns_negative | create regex patterns in negative strand
create_regex_patterns_positive | create regex patterns in positive strand
csAnno-class | Class "csAnno" This class represents the output of epiSeeker Annotation
demo_bmdata | demo base modification data
demo_peak | demo peak file
downloadGEObedFiles | downloadGEObedFiles
downloadGSMbedFiles | downloadGSMbedFiles
dropAnno | dropAnno
enrichAnnoOverlap | enrichAnnoOverlap
enrichPeakOverlap | enrichPeakOverlap
epiSeekerCache | Name of the epiSeeker cache environment (internal static variable)
extend_gr | Extend regions functions
filter.GRanges | Extend filter to Peak (GRanges class object)
getAnnoStat | getAnnoStat
getBioRegion | Prepare a bioregion of selected feature
getBmMatrix | getBmMatrix methods generics
getBmMatrix, | getBmMatrix methods generics
getBmMatrix-method | getBmMatrix methods generics
getBmMatrix.bmData | get the information of base modification
getBmMatrix.BSseq | Get the information of base modification
getGeneAnno | getGeneAnno
getGenomicAnnotation | getGenomicAnnotation
getGEOgenomeVersion | getGEOgenomeVersion
getGEOInfo | getGEOInfo
getGEOspecies | getGEOspecies
getMotifMatrix | Get the information of motif in a range
getNearestFeatureIndicesAndDistances | getNearestFeatureIndicesAndDistances
getPromoters | Get promoter region in GRanges format
getSampleFiles | getSampleFiles
getTagMatrix | getTagMatrix
getTagMatrix.internal | getTagMatrix internal function
getTagMatrix_body | getTagMatrix function for region of body
getTagMatrix_body_internal | get tagmatrix internal function
getTagMatrix_site | getTagMatrix function for region of site
grange2mt | change a list grange object to matrix
gsminfo | Information Datasets
loadTxDb | load defaulst txdb
makeBmDataFromData | makeBmDataFromData method generics
makeBmDataFromData-method | makeBmDataFromData method generics
makeBmDataFromData.internal | makeBmDataFromData.internal
makeBmDataFromFiles | make bmData from files
mutate.GRanges | Extend mutate to Peak (GRanges class object)
overlap | overlap
parse_peak | parse peak str
peakAnno | Example data of peak annotation
peakAnnoList | Example data of a list of peak annotation
plotAnnoBar | plotAnnoBar method generics
plotAnnoBar-method | Class "csAnno" This class represents the output of epiSeeker Annotation
plotAnnoBar-method | plotAnnoBar method generics
plotAnnoBar.data.frame | plotAnnoBar.data.frame
plotAnnoPie | plotAnnoPie method generics
plotAnnoPie-method | Class "csAnno" This class represents the output of epiSeeker Annotation
plotAnnoPie-method | plotAnnoPie method generics
plotAnnoPie.csAnno | plotAnnoPie
plotBmProf | plotBmProf
plotCov | plotCov
plotDistToTSS | plotDistToTSS method generics
plotDistToTSS-method | Class "csAnno" This class represents the output of epiSeeker Annotation
plotDistToTSS-method | plotDistToTSS method generics
plotDistToTSS.data.frame | plotDistToTSS.data.frame
plotGeneTrack | Plot gene track
plotMotifProf | Plot the profile of motif of specific peak
plotPeakHeatmap | plotPeakHeatmap function
plotPeakHeatmap_sub | Plot peak heatmap sub function
plotPeakHeatmap_sub.internal | internal function of plotPeakHeatmap
plotPeakProf | plot peak profile
pwm_obj | motif reference for Homo sapiens
readPeakFile | readPeakFile
rename.GRanges | Rename columns of a GRanges object
seq2gene | seq2gene
seq2gene_result | Result of seq2gene
show | show method
show-method | Class "csAnno" This class represents the output of epiSeeker Annotation
show-method | show method
shuffle | shuffle
subset-method | Class "csAnno" This class represents the output of epiSeeker Annotation
tagMatrix | Example data of tagMatrix
ucsc_release | Information Datasets
upsetplot | upsetplot method
upsetplot-method | Class "csAnno" This class represents the output of epiSeeker Annotation
vennpie | vennpie method generics
vennpie-method | Class "csAnno" This class represents the output of epiSeeker Annotation
vennplot | vennplot
vennplot.peakfile | vennplot.peakfile