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Bioconductor - DMRcate (development version)

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 (3.22)

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 "4.5") 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("DMRcate")
Details biocViews Coverage, DNAMethylation, DataImport, DifferentialExpression, DifferentialMethylation, Epigenetics, GeneExpression, Genetics, GenomeAnnotation, MethylationArray, Microarray, MultipleComparison, OneChannel, Preprocessing, QualityControl, Sequencing, Software, TimeCourse, TwoChannel, WholeGenome Version 3.5.0 In Bioconductor since BioC 2.14 (R-3.1) (11 years) License file LICENSE Depends R (>= 4.3.0) Imports AnnotationHub, ExperimentHub, bsseq, GenomeInfoDb, limma, edgeR, minfi, missMethyl, GenomicRanges, plyr, Gviz, IRanges, stats, utils, S4Vectors, methods, graphics, SummarizedExperiment, biomaRt, grDevices System Requirements URL See More Package Archives

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

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