acde

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

Artificial Components Detection of Differentially Expressed Genes

Bioconductor version: Development (3.21)

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>

Citation (from within R, enter citation("acde")):

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, GeneExpression, Microarray, PrincipalComponent, Software, TimeCourse, mRNAMicroarray
Version	1.37.0
In Bioconductor since	BioC 3.2 (R-3.2) (9 years)
License	GPL-3
Depends	R (>= 3.3), boot (>= 1.3)
Imports	stats, graphics
System Requirements
URL

Suggests	BiocGenerics, RUnit
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Build Report	Build Report

Package Archives

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

Source Package	acde_1.37.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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