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 (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.26.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 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 | methFuse |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | methrix_1.26.0.tar.gz |
| Windows Binary (x86_64) | methrix_1.26.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | methrix_1.26.0.tgz |
| macOS Binary (sonoma-arm64) | methrix_1.26.0.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 |