This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

DMRcate

This is the development version of DMRcate; for the stable release version, see DMRcate.

Methylation array and sequencing spatial analysis methods

Bioconductor version: Development (3.18)

De novo identification and extraction of differentially methylated regions (DMRs) from the human genome using Whole Genome Bisulfite 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 (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("DMRcate")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

Details

biocViews Coverage, DNAMethylation, DataImport, DifferentialExpression, DifferentialMethylation, Epigenetics, GeneExpression, Genetics, GenomeAnnotation, MethylationArray, Microarray, MultipleComparison, OneChannel, Preprocessing, QualityControl, Sequencing, Software, TimeCourse, TwoChannel, WholeGenome
Version 2.15.0
In Bioconductor since BioC 2.14 (R-3.1) (9.5 years)
License file LICENSE
Depends R (>= 4.0.0)
Imports ExperimentHub, bsseq, GenomeInfoDb, limma, edgeR, DSS, minfi, missMethyl, GenomicRanges, plyr, Gviz, IRanges, stats, utils, S4Vectors, methods, graphics, SummarizedExperiment
Linking To
Suggests knitr, RUnit, BiocGenerics, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, FlowSorted.Blood.EPIC, tissueTreg, DMRcatedata
System Requirements
Enhances
URL
See More
Depends On Me ChAMP, methylationArrayAnalysis
Imports Me
Suggests Me missMethyl
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary DMRcate_2.15.0.zip
macOS Binary (x86_64) DMRcate_2.15.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/DMRcate
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DMRcate
Bioc Package Browser https://code.bioconductor.org/browse/DMRcate/
Package Short Url https://bioconductor.org/packages/DMRcate/
Package Downloads Report Download Stats