DAMEfinder

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see DAMEfinder.

Finds DAMEs - Differential Allelicly MEthylated regions

Bioconductor version: 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 iD 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")

DAMEfinder Workflow HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Coverage, DNAMethylation, DifferentialMethylation, Software

Version 1.20.0

In Bioconductor since BioC 3.11 (R-4.0) (5.5 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

Suggests BiocStyle, knitr, rmarkdown, testthat, rtracklayer, BSgenome.Hsapiens.UCSC.hg19

Linking To

Enhances

Depends On Me

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Build Report Build Report

Package Archives

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

Source Package DAMEfinder_1.20.0.tar.gz

Windows Binary (x86_64) DAMEfinder_1.20.0.zip

macOS Binary (x86_64) DAMEfinder_1.20.0.tgz

macOS Binary (arm64) DAMEfinder_1.20.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/DAMEfinder

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DAMEfinder

Bioc Package Browser https://code.bioconductor.org/browse/DAMEfinder/

Package Short Url https://bioconductor.org/packages/DAMEfinder/

Package Downloads Report Download Stats