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| 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 |