methylSig
MethylSig: Differential Methylation Testing for WGBS and RRBS Data
Bioconductor version: 3.23 · Package version: 1.24.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
MethylSig is a package for testing for differentially methylated cytosines (DMCs) or regions (DMRs) in whole-genome bisulfite sequencing (WGBS) or reduced representation bisulfite sequencing (RRBS) experiments. MethylSig uses a beta binomial model to test for significant differences between groups of samples. Several options exist for either site-specific or sliding window tests, and variance estimation.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("methylSig")Details
| Maintainer | Raymond G. Cavalcante <rcavalca@umich.edu> |
| Author | Yongseok Park [aut], Raymond G. Cavalcante [aut, cre] |
| License | GPL-3 |
| Bug Reports | https://github.com/sartorlab/methylSig/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DNAMethylation, DifferentialMethylation, Epigenetics, MethylSeq, Regression, Software |
| Package Short Url | https://bioconductor.org/packages/methylSig/ |
Citation
From within R, enter citation("methylSig"):
Yongseok Park, Raymond G. Cavalcante. methylSig: MethylSig: Differential Methylation Testing for WGBS and RRBS Data. doi:10.18129/B9.bioc.methylSig, R package version 1.24.0, https://bioconductor.org/packages/methylSig.
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 | methylSig_1.24.0.tar.gz |
| Windows binary (x86_64) | methylSig_1.24.0.zip |
| macOS binary (arm64) | methylSig_1.24.0.tgz |
| macOS binary (x86_64) | methylSig_1.24.0.tgz |
Dependencies
Depends: R (>= 3.6)
Imports: bsseq, DelayedArray, DelayedMatrixStats, DSS, IRanges, Seqinfo, GenomicRanges, methods, parallel, stats, S4Vectors
Suggests: BiocStyle, bsseqData, knitr, rmarkdown, testthat (>= 2.1.0), covr