DAMEfinder

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11

Finds DAMEs - Differential Allelicly MEthylated regions

Bioconductor version: Release (3.23)

'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")):

Stephany Orjuela, Dania Machlab, Mark Robinson. DAMEfinder: Finds DAMEs - Differential Allelicly MEthylated regions. doi:10.18129/B9.bioc.DAMEfinder, R package version 1.24.0, https://bioconductor.org/packages/DAMEfinder.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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	1.24.0
In Bioconductor since	BioC 3.11 (R-4.0) (6.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.0)
Imports	stats, Seqinfo, 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
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	DAMEfinder_1.24.0.tar.gz
Windows Binary (x86_64)	DAMEfinder_1.24.0.zip
macOS Binary (big-sur-x86_64)	DAMEfinder_1.24.0.tgz
macOS Binary (sonoma-arm64)	DAMEfinder_1.24.0.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