methrix

Fast and efficient summarization of generic bedGraph files from Bisufite sequencing

Bioconductor version: Release (3.20)

Bedgraph files generated by Bisulfite pipelines often come in various flavors. Critical downstream step requires summarization of these files into methylation/coverage matrices. This step of data aggregation is done by Methrix, including many other useful downstream functions.

Author: Anand Mayakonda [aut, cre] , Reka Toth [aut] , Rajbir Batra [ctb], Clarissa Feuerstein-Akgöz [ctb], Joschka Hey [ctb], Maximilian Schönung [ctb], Pavlo Lutsik [ctb]

Maintainer: Anand Mayakonda <anand_mt at hotmail.com>

Citation (from within R, enter citation("methrix")):

Installation

To install this package, start R (version "4.4") and enter:


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

BiocManager::install("methrix")

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("methrix")

Methrix tutorial	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Coverage, DNAMethylation, Sequencing, Software
Version	1.20.0
In Bioconductor since	BioC 3.10 (R-3.6) (5 years)
License	MIT + file LICENSE
Depends	R (>= 3.6), data.table (>= 1.12.4), SummarizedExperiment
Imports	rtracklayer, DelayedArray, HDF5Array, BSgenome, DelayedMatrixStats, parallel, methods, ggplot2, S4Vectors, matrixStats, graphics, stats, utils, GenomicRanges, IRanges
System Requirements
URL	https://github.com/CompEpigen/methrix
Bug Reports	https://github.com/CompEpigen/methrix/issues

Suggests	knitr, rmarkdown, DSS, bsseq, plotly, BSgenome.Mmusculus.UCSC.mm9, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, BSgenome.Hsapiens.UCSC.hg19, GenomicScores, Biostrings, RColorBrewer, GenomeInfoDb, testthat (>= 2.1.0)
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Build Report	Build Report

Package Archives

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

Source Package	methrix_1.20.0.tar.gz
Windows Binary (x86_64)	methrix_1.20.0.zip
macOS Binary (x86_64)	methrix_1.20.0.tgz
macOS Binary (arm64)	methrix_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/methrix
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/methrix
Bioc Package Browser	https://code.bioconductor.org/browse/methrix/
Package Short Url	https://bioconductor.org/packages/methrix/
Package Downloads Report	Download Stats