Omixer
This is the released version of Omixer; for the devel version, see Omixer.
Omixer: multivariate and reproducible sample randomization to proactively counter batch effects in omics studies
Bioconductor version: Release (3.23)
Omixer - an Bioconductor package for multivariate and reproducible sample randomization, which ensures optimal sample distribution across batches with well-documented methods. It outputs lab-friendly sample layouts, reducing the risk of sample mixups when manually pipetting randomized samples.
Author: Lucy Sinke [cre, aut]
Maintainer: Lucy Sinke <l.j.sinke at lumc.nl>
citation("Omixer")):
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("Omixer")
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("Omixer")| my-vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataRepresentation, ExperimentalDesign, QualityControl, Software, Visualization |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.0.0) |
| Imports | dplyr, ggplot2, forcats, tibble, gridExtra, magrittr, readr, tidyselect, grid, stats, stringr |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/molepi/Omixer/issues |
See More
| Suggests | knitr, rmarkdown, BiocStyle, magick, testthat |
| 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 | Omixer_1.22.0.tar.gz |
| Windows Binary (x86_64) | Omixer_1.22.0.zip |
| macOS Binary (big-sur-x86_64) | Omixer_1.22.0.tgz |
| macOS Binary (sonoma-arm64) | Omixer_1.22.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Omixer |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Omixer |
| Bioc Package Browser | https://code.bioconductor.org/browse/Omixer/ |
| Package Short Url | https://bioconductor.org/packages/Omixer/ |
| Package Downloads Report | Download Stats |