DMRcate

DOI: 10.18129/B9.bioc.DMRcate    

Methylation array and sequencing spatial analysis methods

Bioconductor version: Release (3.13)

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>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("DMRcate")

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("DMRcate")

 

PDF	R Script	The DMRcate package user's guide
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Coverage, DNAMethylation, DataImport, DifferentialExpression, DifferentialMethylation, Epigenetics, GeneExpression, Genetics, GenomeAnnotation, MethylationArray, Microarray, MultipleComparison, OneChannel, Preprocessing, QualityControl, Sequencing, Software, TimeCourse, TwoChannel, WholeGenome
Version	2.6.0
In Bioconductor since	BioC 2.14 (R-3.1) (7.5 years)
License	file LICENSE
Depends	R (>= 3.6.0), minfi, SummarizedExperiment
Imports	ExperimentHub, bsseq, GenomeInfoDb, limma, edgeR, DSS, missMethyl, GenomicRanges, methods, graphics, plyr, Gviz, IRanges, stats, utils, S4Vectors
LinkingTo
Suggests	knitr, RUnit, BiocGenerics, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19
SystemRequirements
Enhances
URL
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	DMRcate_2.6.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)	DMRcate_2.5.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DMRcate
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DMRcate
Package Short Url	https://bioconductor.org/packages/DMRcate/
Package Downloads Report	Download Stats