dmrseq
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing
Bioconductor version: Release (3.17)
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 <keegan at stat.ubc.ca>
citation("dmrseq")):
Installation
To install this package, start R (version "4.3") 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")| Analyzing Bisulfite-seq data with dmrseq | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DNAMethylation, DifferentialMethylation, Epigenetics, FunctionalGenomics, ImmunoOncology, MultipleComparison, Regression, Sequencing, Software, WholeGenome |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (5.5 years) |
| 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 |
| Linking To | |
| Suggests | knitr, rmarkdown, BiocStyle |
| System Requirements | |
| Enhances | |
| URL |
See More
| Depends On Me | |
| Imports Me | biscuiteer |
| Suggests Me | |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | dmrseq_1.20.0.tar.gz |
| Windows Binary | dmrseq_1.20.0.zip |
| macOS Binary (x86_64) | dmrseq_1.20.0.tgz |
| macOS Binary (arm64) | dmrseq_1.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/dmrseq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/dmrseq |
| Bioc Package Browser | https://code.bioconductor.org/browse/dmrseq/ |
| Package Short Url | https://bioconductor.org/packages/dmrseq/ |
| Package Downloads Report | Download Stats |