methrix

DOI: 10.18129/B9.bioc.methrix    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see methrix.

Fast and efficient summarization of generic bedGraph files from Bisufite sequencing

Bioconductor version: 3.15

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	Coverage, DNAMethylation, Sequencing, Software
Version	1.10.0
In Bioconductor since	BioC 3.10 (R-3.6) (3 years)
License	MIT + file LICENSE
Depends	R (>= 3.6), data.table (>= 1.12.4), SummarizedExperiment
Imports	rtracklayer, DelayedArray, HDF5Array, BSgenome, DelayedMatrixStats, parallel, methods, ggplot2, matrixStats, graphics, stats, utils, GenomicRanges, IRanges
LinkingTo
Suggests	knitr, rmarkdown, DSS, bsseq, plotly, BSgenome.Mmusculus.UCSC.mm9, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, GenomicScores, Biostrings, RColorBrewer, GenomeInfoDb, testthat (>= 2.1.0)
SystemRequirements
Enhances
URL	https://github.com/CompEpigen/methrix
BugReports	https://github.com/CompEpigen/methrix/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	methrix_1.10.0.tar.gz
Windows Binary	methrix_1.10.0.zip
macOS Binary (x86_64)	methrix_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/methrix
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/methrix
Package Short Url	https://bioconductor.org/packages/methrix/
Package Downloads Report	Download Stats