BindScore-class         Class "BindScore"
ChIPseqR-package        Identifying Protein Binding Sites in
                        High-Throughput Sequencing Data
RLEBindScore-class      Run-length Encoded Binding Site Scores
RLEReadCounts-class     Run-length Encoded Read Counts
ReadCounts-class        Class "ReadCounts"
alignFeature            Read counts relative to annotated features
callBindingSites-methods
                        Predict protein binding sites from
                        high-throughput sequencing data
compress,ReadCounts-method
                        Compress ReadCount Objects
compress-BindScore      Compress BindScore Objects
compress-methods        Methods for Function compress in Package
                        'ChIPseqR'
decompress              Extract Read Count and Binding Site Score
                        Representations
decompress-methods      Methods for Function decompress in Package
                        'ChIPseqR'
exportBindSequence      Export sequence of predicted binding sites
getBindCor              Calculate cross-correlation between read counts
getBindLen              Estimate length of binding and support region
getCutoff               Determine significance threshold for binding
                        site scores
peaks                   Access slots of S4 classes
pickPeak                Identify peaks above a given threshold
plot,BindScore,missing-method
                        Diagnostic Plots for Binding Site Scores
plot,ReadCounts,missing-method
                        Diagnostic Plots for Read Counts
pos2gff                 Convert genome coordinates into GFF format
simpleNucCall           Predict nucleosome positions from
                        high-throughput sequencing data
startScore              Score potential protein binding sites
strandPileup            Strand specific read counts
windowCounts            Summarize read counts in a sliding window
