OSAT

DOI: 10.18129/B9.bioc.OSAT  

OSAT: Optimal Sample Assignment Tool

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

PDF	R Script	An introduction to OSAT
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataRepresentation, ExperimentalDesign, QualityControl, Software, Visualization
Version	1.46.0
In Bioconductor since	BioC 2.11 (R-2.15) (10.5 years)
License	Artistic-2.0
Depends	methods, stats
Imports
LinkingTo
Suggests	xtable, Biobase
SystemRequirements
Enhances
URL	http://www.biomedcentral.com/1471-2164/13/689
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	OSAT_1.46.0.tar.gz
Windows Binary	OSAT_1.46.0.zip
macOS Binary (x86_64)	OSAT_1.46.0.tgz
macOS Binary (arm64)	OSAT_1.46.0.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