TY - JOUR
T1 - Methrix
T2 - An R/bioconductor package for systematic aggregation and analysis of bisulfite sequencing data
AU - Mayakonda, Anand
AU - Schönung, Maximilian
AU - Hey, Joschka
AU - Batra, Rajbir Nath
AU - Feuerstein-Akgoz, Clarissa
AU - Köhler, Kristin
AU - Lipka, Daniel B.
AU - Sotillo, Rocio
AU - Plass, Christoph
AU - Lutsik, Pavlo
AU - Toth, Reka
N1 - Publisher Copyright:
© 2020 The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: [email protected].
PY - 2020/12/1
Y1 - 2020/12/1
N2 - Motivation: Whole-genome bisulfite sequencing (WGBS) measures DNA methylation at base pair resolution resulting in large bedGraph like coverage files. Current options for processing such files are hindered by discrepancies in file format specification, speed, and memory requirements. Results: We developed methrix, an R package, which provides a toolset for systematic analysis of large datasets. Core functionality of the package includes a comprehensive bedGraph or similar tab-separated text file reader - which summarizes methylation calls based on annotated reference indices, infers and collapses strands and handles uncovered reference CpG sites while facilitating a flexible input file format specification. Additional optimized functions for quality control filtering, subsetting and visualization allow user-friendly and effective processing of WGBS results. Easy integration with tools for differentially methylated region (DMR) calling and annotation further eases the analysis of genome-wide methylation data. Overall, methrix enriches established WGBS workflows by bringing together computational efficiency and versatile functionality.
AB - Motivation: Whole-genome bisulfite sequencing (WGBS) measures DNA methylation at base pair resolution resulting in large bedGraph like coverage files. Current options for processing such files are hindered by discrepancies in file format specification, speed, and memory requirements. Results: We developed methrix, an R package, which provides a toolset for systematic analysis of large datasets. Core functionality of the package includes a comprehensive bedGraph or similar tab-separated text file reader - which summarizes methylation calls based on annotated reference indices, infers and collapses strands and handles uncovered reference CpG sites while facilitating a flexible input file format specification. Additional optimized functions for quality control filtering, subsetting and visualization allow user-friendly and effective processing of WGBS results. Easy integration with tools for differentially methylated region (DMR) calling and annotation further eases the analysis of genome-wide methylation data. Overall, methrix enriches established WGBS workflows by bringing together computational efficiency and versatile functionality.
UR - http://www.scopus.com/inward/record.url?scp=85107862921&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/btaa1048
DO - 10.1093/bioinformatics/btaa1048
M3 - Article
AN - SCOPUS:85107862921
SN - 1367-4803
VL - 36
SP - 5524
EP - 5525
JO - Bioinformatics
JF - Bioinformatics
IS - 22-23
ER -