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Bioconductor - DAMEfinder

DAMEfinder

This is the released version of DAMEfinder; for the devel version, see DAMEfinder.

Finds DAMEs - Differential Allelicly MEthylated regions

Bioconductor version: Release (3.21)

'DAMEfinder' offers functionality for taking methtuple or bismark outputs to calculate ASM scores and compute DAMEs. It also offers nice visualization of methyl-circle plots.

Author: Stephany Orjuela [aut, cre] ORCID: 0000-0002-1508-461X , Dania Machlab [aut], Mark Robinson [aut]

Maintainer: Stephany Orjuela <sorjuelal at gmail.com>

Citation (from within R, enter citation("DAMEfinder")): Installation

To install this package, start R (version "4.5") and enter:


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

BiocManager::install("DAMEfinder")

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("DAMEfinder")
Details biocViews Coverage, DNAMethylation, DifferentialMethylation, Software Version 1.20.0 In Bioconductor since BioC 3.11 (R-4.0) (5 years) License MIT + file LICENSE Depends R (>= 4.0) Imports stats, GenomeInfoDb, GenomicRanges, IRanges, S4Vectors, readr, SummarizedExperiment, GenomicAlignments, stringr, plyr, VariantAnnotation, parallel, ggplot2, Rsamtools, BiocGenerics, methods, limma, bumphunter, Biostrings, reshape2, cowplot, utils System Requirements URL Bug Reports https://github.com/markrobinsonuzh/DAMEfinder/issues See More Package Archives

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

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