ACDtool: a web-server extending the original Audic-Claverie statistical test to the comparison of large data sets of counts

Abstract

AbstractMotivationMore than 20 years ago, our laboratory published an original statistical test (referred to as the Audic-Claverie (AC) test in the literature) to identify differentially expressed genes from the pairwise comparison of counts of cognate RNA-seq reads (then called “expressed sequence tags”) determined in different conditions. Despite its antiquity and the publications of more sophisticated software packages, this original article continued to gather more than 200 citations per year, indicating the persistent usefulness of the simple AC test for the community. This prompted us to propose a fully revamped version of the AC test with a user interface adapted to the diverse and much larger datasets produced by contemporary omics techniques.ResultsWe implemented ACDtool as an interactive, freely accessible web service proposing 3 types of analyses: 1) the pairwise comparison of individual counts, 2) pairwise comparisons of arbitrary large lists of counts, 3) the all-at-once pairwise comparisons of multiple datasets. Statistical computations are implemented using standard R functions and mathematically reformulated as to accommodate all practical ranges of count values. ACDtool can thus analyze datasets from transcriptomic, proteomic, metagenomics, barcoding, ChlP'seq, population genetics, etc, using the same mathematical approach. ACDtool is particularly well suited for comparisons of large datasets without replicates.AvailabilityACDtool is at URL: www.igs.cnrs-mrs.fr/acdtool/ContactJean-Michel.Claverie@univ-amu.frSupplementary informationnone.