OSAT
OSAT: Optimal Sample Assignment Tool
Bioconductor version: Release (3.20)
A sizable genomics study such as microarray often involves the use of multiple batches (groups) of experiment due to practical complication. To minimize batch effects, a careful experiment design should ensure the even distribution of biological groups and confounding factors across batches. OSAT (Optimal Sample Assignment Tool) is developed to facilitate the allocation of collected samples to different batches. With minimum steps, it produces setup that optimizes the even distribution of samples in groups of biological interest into different batches, reducing the confounding or correlation between batches and the biological variables of interest. It can also optimize the even distribution of confounding factors across batches. Our tool can handle challenging instances where incomplete and unbalanced sample collections are involved as well as ideal balanced RCBD. OSAT provides a number of predefined layout for some of the most commonly used genomics platform. Related paper can be find at http://www.biomedcentral.com/1471-2164/13/689 .
Author: Li Yan
Maintainer: Li Yan <li.yan at roswellpark.org>
citation("OSAT")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("OSAT")
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("OSAT")| An introduction to OSAT | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataRepresentation, ExperimentalDesign, QualityControl, Software, Visualization |
| Version | 1.54.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (12 years) |
| License | Artistic-2.0 |
| Depends | methods, stats |
| Imports | |
| System Requirements | |
| URL | http://www.biomedcentral.com/1471-2164/13/689 |
See More
| Suggests | xtable, Biobase |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | designit |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | OSAT_1.54.0.tar.gz |
| Windows Binary (x86_64) | OSAT_1.54.0.zip (64-bit only) |
| macOS Binary (x86_64) | OSAT_1.54.0.tgz |
| macOS Binary (arm64) | OSAT_1.53.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/OSAT |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/OSAT |
| Bioc Package Browser | https://code.bioconductor.org/browse/OSAT/ |
| Package Short Url | https://bioconductor.org/packages/OSAT/ |
| Package Downloads Report | Download Stats |