DAMEfinder

Finds DAMEs - Differential Allelicly MEthylated regions

Bioconductor version: 3.23 · Package version: 1.24.0

'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.

Installation

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

BiocManager::install("DAMEfinder")

Details

Maintainer	Stephany Orjuela <sorjuelal@gmail.com>
Author	Stephany Orjuela [aut, cre] (ORCID: <https://orcid.org/0000-0002-1508-461X>), Dania Machlab [aut], Mark Robinson [aut]
License	MIT + file LICENSE
Bug Reports	https://github.com/markrobinsonuzh/DAMEfinder/issues
Downloads rank	348
Source branch	RELEASE_3_23
biocViews	Coverage, DNAMethylation, DifferentialMethylation, Software

Documentation

DAMEfinder Workflow

Download

Source package

Dependencies

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

Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, BSgenome.Hsapiens.UCSC.hg19