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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 (3.18)

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 "4.3") and enter: 

if (!require("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

Reference Manual PDF

Details

biocViews Coverage, DNAMethylation, Sequencing, Software
Version 1.15.0
In Bioconductor since BioC 3.10 (R-3.6) (4 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
Linking To
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)
System Requirements
Enhances
URL https://github.com/CompEpigen/methrix
Bug Reports https://github.com/CompEpigen/methrix/issues
See More
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
Windows Binary methrix_1.15.0.zip
macOS Binary (x86_64) methrix_1.15.0.tgz
macOS Binary (arm64)
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/
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