# Optimized Functional Annotation Of ChIP-seq Data

## Documentation for package ‘geneXtendeR’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

allPeakLengths | Produces box-and-whisker plot showing distribution of peak lengths across a peaks input file.
annotate | Annotate peaks file.
barChart | Produces bar charts.
cumlinePlot | Produces cumulative line plots.
diffGO | Finds differential gene ontologies
distinct | Finds unique genes under 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