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DAMEfinder

This is the development version of DAMEfinder; for the stable release version, see DAMEfinder.

Finds DAMEs - Differential Allelicly MEthylated regions


Bioconductor version: Development (3.19)

'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>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Coverage, DNAMethylation, DifferentialMethylation, Software
Version 1.15.0
In Bioconductor since BioC 3.11 (R-4.0) (4 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
Suggests BiocStyle, knitr, rmarkdown, testthat, rtracklayer, BSgenome.Hsapiens.UCSC.hg19
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package DAMEfinder_1.15.0.tar.gz
Windows Binary
macOS Binary (x86_64) DAMEfinder_1.15.0.tgz
macOS Binary (arm64)
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