DMCHMM
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see DMCHMM.
Differentially Methylated CpG using Hidden Markov Model
Bioconductor version: 3.9
A pipeline for identifying differentially methylated CpG sites using Hidden Markov Model in bisulfite sequencing data.
Author: Farhad Shokoohi
Maintainer: Farhad Shokoohi <shokoohi at icloud.com>
Citation (from within R, enter
citation("DMCHMM")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DMCHMM")
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("DMCHMM")| DMCHMM | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Coverage, DifferentialMethylation, HiddenMarkovModel, Sequencing, Software |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (6.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.5.0), SummarizedExperiment, methods, S4Vectors, BiocParallel, GenomicRanges, IRanges, fdrtool |
| Imports | utils, stats, grDevices, rtracklayer, multcomp, calibrate, graphics |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/shokoohi/DMCHMM/issues |
See More
| Suggests | testthat, knitr |
| 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 | DMCHMM_1.6.0.tar.gz |
| Windows Binary | DMCHMM_1.6.0.zip |
| Mac OS X 10.11 (El Capitan) | DMCHMM_1.6.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DMCHMM |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DMCHMM |
| Bioc Package Browser | https://code.bioconductor.org/browse/DMCHMM/ |
| Package Short Url | https://bioconductor.org/packages/DMCHMM/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |