ggloor/ALDEx_bioc: Analysis Of Differential Abundance Taking Sample Variation Into Account

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, 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. ALDEx2 also calculates expected standardized effect sizes for paired or unpaired study designs.

Getting started

Package details

AuthorGreg Gloor, Andrew Fernandes, Jean Macklaim, Arianne Albert, Matt Links, Thomas Quinn, Jia Rong Wu, Ruth Grace Wong, Brandon Lieng
Bioconductor views Bayesian ChIPSeq DNASeq DifferentialExpression GeneExpression ImmunoOncology Metagenomics Microbiome RNASeq Sequencing Software Transcriptomics
MaintainerGreg Gloor <>
Licensefile LICENSE
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
ggloor/ALDEx_bioc documentation built on May 10, 2022, 7:14 a.m.