methrix
This is thereleased version of methrix; for the devel version, seemethrix.
Fast and efficient summarization of generic bedGraph files from Bisufite sequencing
Bioconductor version: Release (3.22)
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("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 appropriateBioconductor 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 | 1.24.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (6 years) |
| License | MIT + fileLICENSE |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | methrix_1.24.0.tar.gz |
| Windows Binary (x86_64) | methrix_1.24.0.zip |
| macOS Binary (x86_64) | methrix_1.24.0.tgz |
| macOS Binary (arm64) | methrix_1.24.0.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 |