acde

DOI: 10.18129/B9.bioc.acde  

Artificial Components Detection of Differentially Expressed Genes

Bioconductor version: Release (3.16)

This package provides a multivariate inferential analysis method for detecting differentially expressed genes in gene expression data. It uses artificial components, close to the data's principal components but with an exact interpretation in terms of differential genetic expression, to identify differentially expressed genes while controlling the false discovery rate (FDR). The methods on this package are described in the vignette or in the article 'Multivariate Method for Inferential Identification of Differentially Expressed Genes in Gene Expression Experiments' by J. P. Acosta, L. Lopez-Kleine and S. Restrepo (2015, pending publication).

Author: Juan Pablo Acosta, Liliana Lopez-Kleine

Maintainer: Juan Pablo Acosta <jpacostar at unal.edu.co>

Installation

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

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

BiocManager::install("acde")

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("acde")

 

PDF	R Script	Identification of Differentially Expressed Genes with Artificial Components
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, GeneExpression, Microarray, PrincipalComponent, Software, TimeCourse, mRNAMicroarray
Version	1.28.0
In Bioconductor since	BioC 3.2 (R-3.2) (7.5 years)
License	GPL-3
Depends	R (>= 3.3), boot (>= 1.3)
Imports	stats, graphics
LinkingTo
Suggests	BiocGenerics, RUnit
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	coexnet
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	acde_1.28.0.tar.gz
Windows Binary	acde_1.28.0.zip
macOS Binary (x86_64)	acde_1.28.0.tgz
macOS Binary (arm64)	acde_1.28.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/acde
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/acde
Bioc Package Browser	https://code.bioconductor.org/browse/acde/
Package Short Url	https://bioconductor.org/packages/acde/
Package Downloads Report	Download Stats