dmrseq (original) (raw)

This is the released version of dmrseq; for the devel version, seedmrseq.

Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing

Bioconductor version: Release (3.20)

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.

Author: Keegan Korthauer [cre, aut] , Rafael Irizarry [aut] , Yuval Benjamini [aut], Sutirtha Chakraborty [aut]

Maintainer: Keegan Korthauer

Citation (from within R, enter citation("dmrseq")):

Installation

To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("dmrseq")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("dmrseq")

Details

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Follow Installation instructions to use this package in your R session.