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Bioconductor - methrix

methrix

This is the released version of methrix; for the devel version, see methrix.

Fast and efficient summarization of generic bedGraph files from Bisufite sequencing

Bioconductor version: Release (3.21)

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] ORCID: 0000-0003-1162-687X , Reka Toth [aut] ORCID: 0000-0002-6096-1052 , 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 "4.5") 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")
Details biocViews Coverage, DNAMethylation, Sequencing, Software Version 1.22.1 In Bioconductor since BioC 3.10 (R-3.6) (5.5 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) Linking To Enhances Depends On Me Imports Me Suggests Me methodical Links To Me Build Report Build Report Package Archives

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

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