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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DMRcaller")
In most cases, you don't need to download the package archive at all.
DMRcaller
|
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see DMRcaller.
Differentially Methylated Regions caller
Bioconductor version: 3.3
Uses Bisulfite sequencing data in two conditions and identifies differentially methylated regions between the conditions in CG and non-CG context. The input is the CX report files produced by Bismark and the output is a list of DMRs stored as GRanges objects.
Author: Nicolae Radu Zabet <n.r.zabet at gen.cam.ac.uk> and Jonathan Michael Foonlan Tsang <jmft2 at cam.ac.uk>
Maintainer: Nicolae Radu Zabet <n.r.zabet at gen.cam.ac.uk>
Citation (from within R,
enter citation("DMRcaller")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DMRcaller")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DMRcaller")
| R Script | DMRcaller | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Coverage, DNAMethylation, DifferentialMethylation, Sequencing, Software |
| Version | 1.4.2 |
| In Bioconductor since | BioC 3.1 (R-3.2) (1.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.2), GenomicRanges, IRanges, S4Vectors |
| Imports | parallel, Rcpp, RcppRoll |
| LinkingTo | |
| Suggests | knitr, RUnit, BiocGenerics |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | DMRcaller_1.4.2.tar.gz |
| Windows Binary | DMRcaller_1.4.2.zip |
| Mac OS X 10.9 (Mavericks) | DMRcaller_1.4.2.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/DMRcaller/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/DMRcaller/ |
| Package Downloads Report | Download Stats |
Documentation »
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