OSAT

This is the development version of OSAT; for the stable release version, see OSAT.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11

OSAT: Optimal Sample Assignment Tool

Bioconductor version: Development (3.24)

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 (from within R, enter citation("OSAT")):

Li Yan. OSAT: OSAT: Optimal Sample Assignment Tool. doi:10.18129/B9.bioc.OSAT, R package version 1.61.0, https://bioconductor.org/packages/OSAT.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataRepresentation, ExperimentalDesign, QualityControl, Software, Visualization
Version	1.61.0
In Bioconductor since	BioC 2.11 (R-2.15) (14 years)
License	Artistic-2.0
Depends	methods, stats
Imports
System Requirements
URL	http://www.biomedcentral.com/1471-2164/13/689

Suggests	xtable, Biobase
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	designit
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	OSAT_1.61.0.tar.gz
Windows Binary (x86_64)	OSAT_1.61.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	OSAT_1.61.0.tgz
macOS Binary (sonoma-arm64)	OSAT_1.61.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/OSAT
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/OSAT
Package Short Url	https://bioconductor.org/packages/OSAT/
Package Downloads Report	Download Stats