Bioconductor – ALDEx2

DOI: 10.18129/B9.bioc.ALDEx2  

This package is for version 3.9 of Bioconductor;
for the stable, up-to-date release version, see
ALDEx2.

Analysis Of Differential Abundance Taking Sample Variation Into Account

Bioconductor version: 3.9

A differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard RNA-seq or meta-RNA-seq assays as well as selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, optimized for three or more experimental replicates. The method infers biological and sampling variation to calculate the expected false discovery rate, given the variation, based on a Wilcoxon Rank Sum test and Welch’s t-test (via aldex.ttest), a Kruskal-Wallis test (via aldex.kw), a generalized linear model (via aldex.glm), or a correlation test (via aldex.corr). All tests report p-values and Benjamini-Hochberg corrected p-values.

Author: Greg Gloor, Andrew Fernandes, Jean Macklaim, Arianne Albert, Matt Links, Thomas Quinn, Jia Rong Wu, Ruth Grace Wong,

Maintainer: Greg Gloor <ggloor at uwo.ca>

Installation

To install this package, start R (version
“3.6”) and enter:

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

BiocManager::install("ALDEx2")

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("ALDEx2")

Details

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Installation instructions to use this
package in your R session.