methrix
This package is for version 3.14 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: 3.14
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("methrix")):
Installation
To install this package, start R (version "4.1") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Coverage, DNAMethylation, Sequencing, Software |
| Version | 1.8.0 |
| 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, 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, GenomicScores, Biostrings, RColorBrewer, GenomeInfoDb, testthat (>= 2.1.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | methrix_1.8.0.tar.gz |
| Windows Binary | methrix_1.8.0.zip |
| macOS 10.13 (High Sierra) | methrix_1.8.0.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 |
| Old Source Packages for BioC 3.14 | Source Archive |