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acde

Artificial Components Detection of Differentially Expressed Genes


Bioconductor version: Release (3.19)

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 "4.4") 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")
Identification of Differentially Expressed Genes with Artificial Components PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, GeneExpression, Microarray, PrincipalComponent, Software, TimeCourse, mRNAMicroarray
Version 1.34.0
In Bioconductor since BioC 3.2 (R-3.2) (8.5 years)
License GPL-3
Depends R (>= 3.3), boot (>= 1.3)
Imports stats, graphics
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Suggests BiocGenerics, RUnit
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Package Archives

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

Source Package acde_1.34.0.tar.gz
Windows Binary acde_1.34.0.zip (64-bit only)
macOS Binary (x86_64) acde_1.34.0.tgz
macOS Binary (arm64) acde_1.34.0.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/
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