DAMEfinder

DOI: 10.18129/B9.bioc.DAMEfinder    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see DAMEfinder.

Finds DAMEs - Differential Allelicly MEthylated regions

Bioconductor version: 3.14

'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] , Dania Machlab [aut], Mark Robinson [aut]

Maintainer: Stephany Orjuela <sorjuelal at gmail.com>

Installation

To install this package, start R (version "4.1") 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")

 

HTML	R Script	DAMEfinder Workflow
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Coverage, DNAMethylation, DifferentialMethylation, Software
Version	1.6.0
In Bioconductor since	BioC 3.11 (R-4.0) (2 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
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat, rtracklayer, BSgenome.Hsapiens.UCSC.hg19
SystemRequirements
Enhances
URL
BugReports	https://github.com/markrobinsonuzh/DAMEfinder/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	DAMEfinder_1.6.0.tar.gz
Windows Binary	DAMEfinder_1.6.0.zip
macOS 10.13 (High Sierra)	DAMEfinder_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DAMEfinder
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DAMEfinder
Package Short Url	https://bioconductor.org/packages/DAMEfinder/
Package Downloads Report	Download Stats