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bioconductor-benchdamic

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Benchmark of differential abundance methods on microbiome data

Installation

To install this package, run one of the following:

Conda
$conda install bioconda::bioconductor-benchdamic

Usage Tracking

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Description

Starting from a microbiome dataset (16S or WMS with absolute count values) it is possible to perform several analysis to assess the performances of many differential abundance detection methods. A basic and standardized version of the main differential abundance analysis methods is supplied but the user can also add his method to the benchmark. The analyses focus on 4 main aspects: i) the goodness of fit of each method's distributional assumptions on the observed count data, ii) the ability to control the false discovery rate, iii) the within and between method concordances, iv) the truthfulness of the findings if any apriori knowledge is given. Several graphical functions are available for result visualization.

About

Summary

Benchmark of differential abundance methods on microbiome data

Last Updated

Jul 18, 2023 at 16:59

License

Artistic-2.0

Total Downloads

6.0K

Supported Platforms

noarch