bioconductor-aldex2

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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.

Home http://bioconductor.org/packages/3.6/bioc/html/ALDEx2.html
Versions 1.10.0, 1.8.0
License file LICENSE
Recipe https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-aldex2

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-aldex2

and update with:

conda update bioconductor-aldex2

docker

A Docker container is available at https://quay.io/repository/biocontainers/bioconductor-aldex2.