methrix

DOI: 10.18129/B9.bioc.methrix    

This is the development version of methrix; for the stable release version, see methrix.

Fast and efficient summarization of generic bedGraph files from Bisufite sequencing

Bioconductor version: Development (3.11)

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], Maximilian Schönung [ctb], Pavlo Lutsik [ctb], Joschka Hey [ctb]

Maintainer: Anand Mayakonda <anand_mt at hotmail.com>

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

Installation

To install this package, start R (version "4.0") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.1.0
In Bioconductor since BioC 3.10 (R-3.6) (< 6 months)
License MIT + file LICENSE
Depends R (>= 3.6), data.table (>= 1.12.4), SummarizedExperiment
Imports DelayedArray, HDF5Array, BSgenome, rjson, DelayedMatrixStats, parallel, methods, ggplot2, matrixStats, graphics, stats, utils
LinkingTo
Suggests knitr, rmarkdown, DSS, bsseq, plotly, BSgenome.Mmusculus.UCSC.mm9, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, GenomicScores, Biostrings, RColorBrewer, GenomicRanges, GenomeInfoDb, IRanges, testthat (>= 2.1.0)
SystemRequirements
Enhances
URL
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_1.1.0.tar.gz
Windows Binary methrix_1.1.0.zip
Mac OS X 10.11 (El Capitan) methrix_1.1.0.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

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