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DMRcate

Methylation array and sequencing spatial analysis methods


Bioconductor version: Release (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")

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

Details

biocViews Coverage, DNAMethylation, DataImport, DifferentialExpression, DifferentialMethylation, Epigenetics, GeneExpression, Genetics, GenomeAnnotation, MethylationArray, Microarray, MultipleComparison, OneChannel, Preprocessing, QualityControl, Sequencing, Software, TimeCourse, TwoChannel, WholeGenome
Version 2.16.1
In Bioconductor since BioC 2.14 (R-3.1) (10 years)
License file LICENSE
Depends R (>= 4.0.0)
Imports ExperimentHub, bsseq, GenomeInfoDb, limma, edgeR, minfi, missMethyl, GenomicRanges, plyr, Gviz, IRanges, stats, utils, S4Vectors, methods, graphics, SummarizedExperiment, biomaRt
System Requirements
URL
See More
Suggests knitr, RUnit, BiocGenerics, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, FlowSorted.Blood.EPIC, tissueTreg, DMRcatedata
Linking To
Enhances
Depends On Me ChAMP, methylationArrayAnalysis
Imports Me
Suggests Me missMethyl
Links To Me
Build Report Build Report

Package Archives

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

Source Package DMRcate_2.16.1.tar.gz
Windows Binary DMRcate_2.16.1.zip (64-bit only)
macOS Binary (x86_64) DMRcate_2.16.1.tgz
macOS Binary (arm64) DMRcate_2.16.1.tgz
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