DMRcate
Methylation array and sequencing spatial analysis methods
Bioconductor version: 3.23 · Package version: 3.8.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DMRcate")Details
| Maintainer | Tim Peters <t.peters@garvan.org.au> |
| Author | Tim Peters |
| License | file LICENSE |
| Downloads rank | 1362 |
| Source branch | RELEASE_3_23 |
| biocViews | Coverage, DNAMethylation, DataImport, DifferentialExpression, DifferentialMethylation, Epigenetics, GeneExpression, Genetics, GenomeAnnotation, MethylationArray, Microarray, MultipleComparison, OneChannel, Preprocessing, QualityControl, Sequencing, Software, TimeCourse, TwoChannel, WholeGenome |
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Dependencies
Depends: R (>= 4.3.0)
Imports: AnnotationHub, ExperimentHub, bsseq, Seqinfo, limma, edgeR, minfi, missMethyl, GenomicRanges, plyr, Gviz, IRanges, stats, utils, S4Vectors, methods, graphics, SummarizedExperiment, biomaRt, grDevices
Suggests: knitr, RUnit, BiocGenerics, GenomeInfoDb, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICv2anno.20a1.hg38, FlowSorted.Blood.EPIC, tissueTreg, DMRcatedata, EPICv2manifest
Reverse dependencies
Depends On Me (2): ChAMP, methylationArrayAnalysis
Suggests Me (2): easyEWAS, missMethyl