DAMEfinder
Finds DAMEs - Differential Allelicly MEthylated regions
Bioconductor version: Release (3.20)
'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")
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 | 1.18.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4.5 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 |
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_1.18.0.tar.gz |
| Windows Binary (x86_64) | DAMEfinder_1.18.0.zip |
| macOS Binary (x86_64) | DAMEfinder_1.18.0.tgz |
| macOS Binary (arm64) | DAMEfinder_1.18.0.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 |