I was trying to sum up some of the development work done on FindPeaks in April-June this year for a quarterly report and ended up writing the following text. Maybe someone will be inspired by it to give the package a shot. (=
FindPeaks now includes Control and Compare modes that operate to identify features that differ in statistically significant ways between a sample and a control or two samples. In the Control mode, only those locations which differ significantly with greater enrichment in the sample are preserved, whereas Compare mode identifies areas of differing enrichment in both the sample and the control. This method uses peak pairing and linear regression methods that are symmetrical (resulting in identical peak pairing and statistics regardless of the order of the data sets presented). These methods can be used in a wide variety of situations including ChIP-Seq, RNA-Seq and even in copy number variation analysis for whole genome comparative analysis.
FindFeatures is a new application in the FindPeaks/Vancouver Short Read Analysis Package that allows peaks identified by the FindPeaks application to be mapped to annotated features on the genome of interest contained in the Ensembl database. This tool set uses the peaks files produced by the FindPeaks application to convert the relevant locations to a generic - bedfile-like format, which can then be used to identify any genes (introns or exons) to which they map. This may also be used to identify areas upstream of genes, or in close proximity to other features of interest.