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DAMEfinder
This is thereleased version of DAMEfinder; for the devel version, seeDAMEfinder.
Finds DAMEs - Differential Allelicly MEthylated regions
Bioconductor version: Release (3.22)
'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("DAMEfinder")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("DAMEfinder")For older versions of R, please refer to the appropriateBioconductor 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 | 1.22.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (5.5 years) |
| License | MIT + fileLICENSE |
| 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 |
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
FollowInstallation instructions to use this package in your R session.
| Source Package | DAMEfinder_1.22.0.tar.gz |
| Windows Binary (x86_64) | DAMEfinder_1.22.0.zip |
| macOS Binary (x86_64) | DAMEfinder_1.22.0.tgz |
| macOS Binary (arm64) | DAMEfinder_1.22.0.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 |