wateRmelon
This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see wateRmelon.
Illumina 450 and EPIC methylation array normalization and metrics
Bioconductor version: 3.14
15 flavours of betas and three performance metrics, with methods for objects produced by methylumi and minfi packages.
Author: Leo C Schalkwyk [cre, aut], Tyler J Gorrie-Stone [aut], Ruth Pidsley [aut], Chloe CY Wong [aut], Nizar Touleimat [ctb], Matthieu Defrance [ctb], Andrew Teschendorff [ctb], Jovana Maksimovic [ctb], Louis Y El Khoury [ctb], Yucheng Wang [ctb]
Maintainer: Leo C Schalkwyk <lschal at essex.ac.uk>
citation("wateRmelon")):
Installation
To install this package, start R (version "4.1") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("wateRmelon")
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("wateRmelon")| wateRmelon User's Guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, Microarray, Preprocessing, QualityControl, Software, TwoChannel |
| Version | 2.0.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (11 years) |
| License | GPL-3 |
| Depends | R (>= 3.5.0), Biobase, limma, methods, matrixStats, methylumi, lumi, ROC, IlluminaHumanMethylation450kanno.ilmn12.hg19, illuminaio |
| Imports | Biobase |
| System Requirements | |
| URL |
See More
| Suggests | RPMM, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BiocStyle, knitr, rmarkdown, IlluminaHumanMethylationEPICmanifest, irlba, FlowSorted.Blood.EPIC, FlowSorted.Blood.450k, preprocessCore |
| Linking To | |
| Enhances | minfi |
| Depends On Me | bigmelon, skewr |
| Imports Me | ChAMP, MEAT |
| Suggests Me | RnBeads |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | wateRmelon_2.0.0.tar.gz |
| Windows Binary | wateRmelon_2.0.0.zip |
| macOS 10.13 (High Sierra) | wateRmelon_2.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/wateRmelon |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/wateRmelon |
| Bioc Package Browser | https://code.bioconductor.org/browse/wateRmelon/ |
| Package Short Url | https://bioconductor.org/packages/wateRmelon/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.14 | Source Archive |