allPeakLengths          Produces box-and-whisker plot showing
                        distribution of peak lengths across a peaks
                        input file.
annotate                Annotate peaks file.
annotate_n              Annotate peaks file.
barChart                Produces bar charts.
cumlinePlot             Produces cumulative line plots.
diffGO                  Finds differential gene ontologies
distinct                Finds unique genes under peaks.
gene_annotate           Annotate peak file based on gene.
gene_lookup             Looks up specific gene and closest peaks
hotspotPlot             Graphs hotspots of statistically significant
                        peak activity.
linePlot                Produces line plots.
makeNetwork             Makes gene-GO networks
makeWordCloud           Makes word cloud from gene ontology terms
meanPeakLength          Calculates mean (average) peak length for any
                        genomic region.
meanPeakLengthPlot      Produces line plots of mean (average) peak
                        length within any genomic interval.
peakLengthBoxplot       Produces box-and-whisker plot of peak lengths
                        within any genomic interval.
peaksInput              Preprocesses a peaks input file.
peaksMerge              Transform peaks into merged peaks.
plotWordFreq            Plots word frequencies found within gene
                        ontology terms
rat                     Gene transfer format (GTF) file for rat
                        (Rattus_norvegicus.Rnor_6.0.84)
samplepeaksinput        Sample peaks list to be used as input to
                        geneXtendeR
