DAMEfinder
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see DAMEfinder.
Finds DAMEs - Differential Allelicly MEthylated regions
Bioconductor version: 3.13
'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("DAMEfinder")
):
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")
DAMEfinder Workflow | HTML | R Script |
Reference Manual | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | Coverage, DNAMethylation, DifferentialMethylation, Software |
Version | 1.4.0 |
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_1.4.0.tar.gz |
Windows Binary | DAMEfinder_1.4.0.zip |
macOS 10.13 (High Sierra) | DAMEfinder_1.4.0.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 |
Old Source Packages for BioC 3.13 | Source Archive |