| annotate | Annotate peaks file. |
| barChart | Produces bar charts. |
| distinct | Finds unique genes under peaks. |
| linePlot | Produces line plots. |
| peaksInput | Preprocesses a peaks input file. |
| 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 |