DOI: 10.18129/B9.bioc.dmrseq    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see dmrseq.

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

Bioconductor version: 3.8

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 <keegan at>, Sutirtha Chakraborty <statistuta at>, Yuval Benjamini <yuvalbenj at>, Rafael Irizarry <rafa at>

Maintainer: Keegan Korthauer <keegan at>

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biocViews DNAMethylation, DifferentialMethylation, Epigenetics, FunctionalGenomics, ImmunoOncology, MultipleComparison, Regression, Sequencing, Software, WholeGenome
Version 1.2.5
In Bioconductor since BioC 3.7 (R-3.5) (1 year)
License MIT + file LICENSE
Depends R (>= 3.5), bsseq
Imports GenomicRanges, nlme, ggplot2, S4Vectors, RColorBrewer, bumphunter, DelayedMatrixStats(>= 1.1.13), matrixStats, BiocParallel, outliers, methods, locfit, IRanges, grDevices, graphics, stats, utils, annotatr, AnnotationHub, rtracklayer, GenomeInfoDb, splines
Suggests knitr, rmarkdown, BiocStyle
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