ChIPSeqSpike: A R/Bioconductor package for ChIP-Seq data scaling according to spike-in control

Abstract

MotivationChromatin Immuno-Precipitation followed by Sequencing (ChlP-Seq) is used to determine the binding sites of any protein of interest. ChIP-Seq data suffer from being more qualitative than quantitative. The recent use of Spike-in controls along with the standard protocol tackled this problem. However, no dedicated tool is available for a robust evaluation of this new ChIP-seq approach\n\nResultsWe developed ChIPSeqSpike, an R/Bioconductor package that enables ChIP-Seq spike-in normalization, assessment and analysis. Ready to use scaled bigwig files and scaling factors values are obtained as output. ChIPSeqSpike also provides tools for ChIP-Seq spike-in assessment and analysis through a versatile collection of graphical functions.\n\nAvailabilityThe package is implemented in R (as of version 3.4) and is available from Bioconductor at the URL: https://www.bioconductor.org/packages/3.7/bioc/html/ChIPSeqSpike.html, where installation and usage instructions can be found.\n\nContactnicolas.descostes@nyumc.org