A differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard RNAseq or metaRNAseq assays as well as selected and unselected values from invitro sequence selections. Uses a Dirichletmultinomial 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 Wilcox rank test or Welch ttest (via aldex.ttest), or a glm and KruskalWallis test (via aldex.glm). Reports pvalues and BenjaminiHochberg corrected pvalues.
Package details 


Author  Greg Gloor, Ruth Grace Wong, Andrew Fernandes, Arianne Albert, Matt Links, Thomas Quinn, Jia Rong Wu 
Bioconductor views  Bayesian ChIPSeq DNASeq DifferentialExpression GeneExpression Metagenomics Microbiome RNASeq Sequencing Software 
Maintainer  Greg Gloor <[email protected]> 
License  file LICENSE 
Version  1.12.0 
URL  https://github.com/ggloor/ALDEx2 
Package repository  View on Bioconductor 
Installation 
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