DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts.

ABSTRACT: DNA methylation has been associated with transcriptional repression and detection of differential methylation is important in understanding the underlying causes of differential gene expression. Bisulfite-converted genomic DNA sequencing is the current gold standard in the field for building genome-wide maps at a base pair resolution of DNA methylation. Here we systematically investigate the underlying features of detecting differential DNA methylation in CpG and non-CpG contexts, considering both the case of mammalian systems and plants. In particular, we introduce DMRcaller, a highly efficient R/Bioconductor package, which implements several methods to detect differentially methylated regions (DMRs) between two samples. Most importantly, we show that different algorithms are required to

SUBMITTER: Catoni M 

PROVIDER: S-EPMC6212837 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature