calculateStrandCoverage
                        Calculate the strand information based on
                        coverage
calculateStrandNbReads
                        Calculate the strand information based the
                        number of reads
checkPairedEnd          Test whether a bam file if single end or paired
                        end
concatenateAlignments   Concatenate a list of Alignments into One
filterDNA               Filter Double Strand Sequences from a Bam File
getWinFromBamFile       get the strand information of all windows from
                        bam files
getWinFromGranges       Get the Sliding Windows from a GRanges object
getWinFromIRanges       Get the Ranges of Sliding Windows from an
                        IRanges object
getWinFromReadInfo      get the strand information of all windows from
                        read information
getWinOfAlignments      get the window ranges of alignments
intersectWithFeature    Intersect the windows data frame with an
                        annotation data frame
keptProbaWin            get the probability of begin kept for each
                        window
keptReadFragment        calculate the read fragments to be kept
plotHist                Plot the histogram of positive proportions
plotWin                 Plot the Proportion of + Stranded Reads
strandCheckR-package    Quantify and Filter putative double strand DNA
                        from strand-specific RNA bam file
summarizeHist           Summarize the histogram of strand proportions
                        from the input windows data frame
