chroGPS2: differential analysis of epigenome maps in R.

Abstract

1In the last years, after systematic mapping of epigenomics data from multiple organisms, tissues and cell lines, the ability to efficiently integrate, visualize and compare such information remains a challenge. Here we present chroGPS version 2, a major update of our previously developed software chroGPS, for visualization and differential analysis of epigenomes. Methods are provided for efficient integration and comparison of data from different conditions or biological backgrounds, accounting and adjusting for systematic biases in order to provide an efficient and statistically robust base for differential analysis. We also include functionalities for general data assessment and quality control prior to comparing maps, such as functions to study chromatin domain conservation between epigenomic backgrounds, to detect gross technical outliers and also to help in the selection of candidate marks for de-novo epigenome mapping.\n\nAvailabilityhttps://www.bioconductor.org/packages/release/bioc/html/chroGPS.html - Contact: oscar.reina@irbbarcelona.org