Aldex: ANOVA-like RNA-seq analysis

Adlex is an RNA-seq tool that uses the Dirichlet distribution and a transformation to identify genes that exhibit small within-condition and large between-condition variance.
The package was developed specifically for multiple-organism RNA-Seq data generated by high-throughput sequencing platforms (meta-RNA-Seq), but testing showed that it performed very well with traditional RNA-Seq datasets. In principle, the analysis method should be applicable to any type of count data that is generated by high-throughput sequencing such as ChIP-Seq or sequencing of metagenomes, although ALDEx has not been tested on these types of problems as of yet.

The ALDEx package is suitable for comparison of samples between two conditions where there are at least two biological replicates per condition. One unique feature of ALDEx is the explicit estimation of the within-sample biological variation using the Dirichlet distribution. This distri- bution maintains the proportional nature of the data, which is not the case for Poisson or negative- binomial based methods. The second unique feature of ALDEx is that it introduces a mathematical transform to normalize the data by removing the uninformative subspace introduced by logarith- mic transformation.

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