MethCP
This package is for version 3.10 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see MethCP.
Differential methylation anlsysis for bisulfite sequencing data
Bioconductor version: 3.10
MethCP is a differentially methylated region (DMR) detecting method for whole-genome bisulfite sequencing (WGBS) data, which is applicable for a wide range of experimental designs beyond the two-group comparisons, such as time-course data. MethCP identifies DMRs based on change point detection, which naturally segments the genome and provides region-level differential analysis.
Author: Boying Gong [aut, cre]
Maintainer: Boying Gong <jorothy_gong at berkeley.edu>
citation("MethCP")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MethCP")
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("MethCP")| methcp: User’s Guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialMethylation, Sequencing, Software, TimeCourse, WholeGenome |
| Version | 1.0.2 |
| In Bioconductor since | BioC 3.10 (R-3.6) (4.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.6.0) |
| Imports | methods, utils, stats, S4Vectors, bsseq, DSS, methylKit, DNAcopy, GenomicRanges, IRanges, GenomeInfoDb, BiocParallel |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/boyinggong/methcp/issues |
See More
| Suggests | testthat, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MethCP_1.0.2.tar.gz |
| Windows Binary | MethCP_1.0.0.zip |
| Mac OS X 10.11 (El Capitan) | MethCP_1.0.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MethCP |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MethCP |
| Bioc Package Browser | https://code.bioconductor.org/browse/MethCP/ |
| Package Short Url | https://bioconductor.org/packages/MethCP/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.10 | Source Archive |