.                       .
.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
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.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_body       getTagMatrix function for region of body
getTagMatrix_body_internal
                        get tagmatrix internal function
getTagMatrix_site       getTagMatrix function for region of site
getTagMatrix.internal   getTagMatrix internal function
grange2mt               change a list grange object to matrix
gsminfo                 Information Datasets
loadTxDb                load defaulst txdb
makeBmDataFromData      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.data.frame
                        plotAnnoBar.data.frame
plotAnnoPie             plotAnnoPie method generics
plotAnnoPie.csAnno      plotAnnoPie
plotBmProf              plotBmProf
plotCov                 plotCov
plotDistToTSS           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
shuffle                 shuffle
tagMatrix               Example data of tagMatrix
upsetplot               upsetplot method
vennpie                 vennpie method generics
vennplot                vennplot
vennplot.peakfile       vennplot.peakfile
