PCBS: an R package for fast and accurate analysis of bisulfite sequencing data

Motivation Whole-genome bisulfite sequencing is a powerful tool for analyzing chromatin methylation genome-wide, but analysis of whole-genome bisulfite data is hampered by slow, inaccurate, and inflexible pipelines. Results We developed PCBS, a computationally efficient R package for Whole Genome Bisulfite Sequencing analysis that demonstrates remarkable accuracy and flexibility compared to current tools. PCBS identifies differentially methylated loci and differentially methylated regions and offers novel functionality that allows for more targeted methylation analyses. PCBS uses minimal computational resources; a complete pipeline in mouse can run on a local RStudio instance in a matter of minutes. Availability and Implementation PCBS is an R package available under a GNU GPLv3 license at: https://github.com/katlande/PCBS and from CRAN: https://CRAN.R-project.org/package=PCBS . Instructions for use are available at: https://katlande.github.io/PCBS/ . Supplementary Information “Supplementary data are available on BioRXiv.”