Optimized Functional Annotation Of ChIP-seq Data

Documentation for package ‘geneXtendeR’ version 1.30.0

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