ALDEx2: Analysis Of Differential Abundance Taking Sample Variation Into Account
Version 1.8.0

A differential abundance analysis for the comparison of two or more conditions. For example, single-organism and meta-RNA-seq high-throughput sequencing assays, or of selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected false discovery rate given the biological and sampling variation using the Wilcox rank test or Welches t-test (aldex.ttest) or the glm and Kruskal Wallis tests (aldex.glm). Reports both P and fdr values calculated by the Benjamini Hochberg correction.

Package details

AuthorGreg Gloor, Ruth Grace Wong, Andrew Fernandes, Arianne Albert, Matt Links, Jia Rong Wu
Bioconductor views Bayesian ChIPSeq DNASeq DifferentialExpression GeneExpression Metagenomics Microbiome RNASeq Sequencing Software
MaintainerGreg Gloor <ggloor@uwo.ca>
Licensefile LICENSE
Version1.8.0
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ALDEx2")

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ALDEx2 documentation built on May 31, 2017, 11:50 a.m.