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 Wilcox rank test or Welch t-test (via aldex.ttest), or a glm and Kruskal-Wallis test (via aldex.glm). Reports p-values and Benjamini-Hochberg corrected p-values.
|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]>|
|Package repository||View on Bioconductor|
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