DMRcate
Methylation array and sequencing spatial analysis methods
Bioconductor version: Release (3.20)
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("DMRcate")):
Installation
To install this package, start R (version "4.4") 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")| DMR calling from EPICv2 arrays | R Script | |
| DMRcate for bisulfite sequencing assays (WGBS and RRBS) | R Script | |
| DMRcate for EPICv1 and 450K assays | R Script | |
| Reference Manual | ||
| 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 | 3.2.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (10.5 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
| Suggests | knitr, RUnit, BiocGenerics, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICv2anno.20a1.hg38, FlowSorted.Blood.EPIC, tissueTreg, DMRcatedata, EPICv2manifest |
| Linking To | |
| Enhances | |
| Depends On Me | 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_3.2.0.tar.gz |
| Windows Binary (x86_64) | DMRcate_3.2.0.zip |
| macOS Binary (x86_64) | DMRcate_3.2.0.tgz |
| macOS Binary (arm64) | DMRcate_3.1.10.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 |