PREDA: an R-package to identify regional variations in genomic data.

SUMMARY: Chromosomal patterns of genomic signals represent molecular fingerprints that may reveal how the local structural organization of a genome impacts the functional control mechanisms. Thus, the integrative analysis of multiple sources of genomic data and information deepens the resolution and enhances the interpretation of stand-alone high-throughput data. In this note, we present PREDA (Position RElated Data Analysis), an R package for detecting regional variations in genomics data. PREDA identifies relevant chromosomal patterns in high-throughput data using a smoothing approach that accounts for distance and density variability of genomics features. Custom-designed data structures allow efficiently managing diverse signals in different genomes. A variety of smoothing functions and statistics empower flexible and robust workflows. The modularity of package design allows an easy deployment of custom analytical pipelines. Tabular and graphical representations facilitate downstream biological interpretation of results. AVAILABILITY: PREDA is available in Bioconductor and at http://www.xlab.unimo.it/PREDA. CONTACT: silvio.bicciato@unimore.it SUPPLEMENTARY INFORMATION: Supplementary information is available at Bioinformatics online.