kdkorthauer/dmrseq: Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing

This package implements an approach for scanning the genome to detect and perform accurate inference on differentially methylated regions from Whole Genome Bisulfite Sequencing data. The method is based on comparing detected regions to a pooled null distribution, that can be implemented even when as few as two samples per population are available. Region-level statistics are obtained by fitting a generalized least squares (GLS) regression model with a nested autoregressive correlated error structure for the effect of interest on transformed methylation proportions.

Getting started

Package details

AuthorKeegan Korthauer <[email protected]>, Sutirtha Chakraborty <[email protected]>, Yuval Benjamini <[email protected]>, Rafael Irizarry <[email protected]>
Bioconductor views DNAMethylation DifferentialMethylation Epigenetics FunctionalGenomics MultipleComparison Regression Sequencing Software WholeGenome
MaintainerKeegan Korthauer <[email protected]>
LicenseMIT + file LICENSE
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
kdkorthauer/dmrseq documentation built on Dec. 6, 2018, 11:21 p.m.