methrix

This package is for version 3.10 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: 3.10

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 "3.6") 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

Details

biocViews Coverage, DNAMethylation, Sequencing, Software
Version 1.0.05
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
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
System Requirements
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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)
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Package Archives

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

Source Package methrix_1.0.05.tar.gz
Windows Binary methrix_1.0.05.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) methrix_1.0.05.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
Old Source Packages for BioC 3.10 Source Archive