dmrseq
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing
Bioconductor version: 3.24 · Package version: 1.33.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("dmrseq")Details
| Maintainer | Keegan Korthauer <keegan@stat.ubc.ca> |
| Author | Keegan Korthauer [cre, aut] (ORCID: <https://orcid.org/0000-0002-4565-1654>), Rafael Irizarry [aut] (ORCID: <https://orcid.org/0000-0002-3944-4309>), Yuval Benjamini [aut], Sutirtha Chakraborty [aut] |
| License | MIT + file LICENSE |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DNAMethylation, DifferentialMethylation, Epigenetics, FunctionalGenomics, ImmunoOncology, MultipleComparison, Regression, Sequencing, Software, WholeGenome |
| Package Short Url | https://bioconductor.org/packages/dmrseq/ |
Citation
From within R, enter citation("dmrseq"):
Keegan Korthauer, Rafael Irizarry, Yuval Benjamini, Sutirtha Chakraborty. dmrseq: Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing. doi:10.18129/B9.bioc.dmrseq, R package version 1.33.0, https://bioconductor.org/packages/dmrseq.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | dmrseq_1.33.0.tar.gz |
| Windows binary (x86_64) | dmrseq_1.33.0.zip |
| macOS binary (arm64) | dmrseq_1.33.0.tgz |
| macOS binary (x86_64) | dmrseq_1.33.0.tgz |
Dependencies
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, Seqinfo, splines
Suggests: knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
Reverse dependencies
Imports Me (1): biscuiteer