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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 (3.20)

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")

# 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")
Methrix tutorial HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Coverage, DNAMethylation, Sequencing, Software
Version 1.19.0
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 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
See More
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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Package Archives

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

Source Package methrix_1.19.0.tar.gz
Windows Binary methrix_1.19.0.zip
macOS Binary (x86_64) methrix_1.19.0.tgz
macOS Binary (arm64) methrix_1.19.0.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