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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("DMRcate")
In most cases, you don't need to download the package archive at all.
DMRcate
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Methylation array and sequencing spatial analysis methods
Bioconductor version: Release (3.5)
De novo identification and extraction of differentially methylated regions (DMRs) from the human genome using Whole Genome Bisulphite Sequencing (WGBS) and Illumina Infinium Array (450K and EPIC) data. Provides functionality for filtering probes possibly confounded by SNPs and cross-hybridisation. Includes GRanges generation and plotting functions.
Author: Tim Peters
Maintainer: Tim Peters <t.peters at garvan.org.au>
Citation (from within R,
enter citation("DMRcate")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DMRcate")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DMRcate")
| R Script | The DMRcate package user's guide | |
| Reference Manual | ||
| Text | NEWS | |
| Text | LICENSE |
Details
| biocViews | DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, Genetics, GenomeAnnotation, MethylationArray, Microarray, MultipleComparison, OneChannel, QualityControl, Software, TimeCourse, TwoChannel |
| Version | 1.12.1 |
| In Bioconductor since | BioC 2.14 (R-3.1) (3.5 years) |
| License | file LICENSE |
| Depends | R (>= 3.3.0), minfi, DSS, DMRcatedata |
| Imports | limma, missMethyl, GenomicRanges, parallel, methods, graphics, plyr, Gviz, IRanges, stats, utils, S4Vectors |
| LinkingTo | |
| Suggests | knitr, RUnit, BiocGenerics, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19 |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | ChAMP |
| Imports Me | MEAL |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DMRcate_1.12.1.tar.gz |
| Windows Binary | DMRcate_1.12.1.zip |
| Mac OS X 10.11 (El Capitan) | DMRcate_1.12.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DMRcate |
| Package Short Url | http://bioconductor.org/packages/DMRcate/ |
| Package Downloads Report | Download Stats |
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