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. 2023 Jan 1;39(1):btac778.
doi: 10.1093/bioinformatics/btac778.

benchdamic: benchmarking of differential abundance methods for microbiome data

Matteo Calgaro  1 , Chiara Romualdi  2 , Davide Risso  3 , Nicola Vitulo  1
Affiliations

benchdamic: benchmarking of differential abundance methods for microbiome data

Matteo Calgaro et al. Bioinformatics. .

Abstract

Summary: Recently, an increasing number of methodological approaches have been proposed to tackle the complexity of metagenomics and microbiome data. In this scenario, reproducibility and replicability have become two critical issues, and the development of computational frameworks for the comparative evaluations of such methods is of utmost importance. Here, we present benchdamic, a Bioconductor package to benchmark methods for the identification of differentially abundant taxa.

Availability and implementation: benchdamic is available as an open-source R package through the Bioconductor project at https://bioconductor.org/packages/benchdamic/.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
Graphical abstract. Each box on the right represents a step of the analysis where information about the research question, type of input data, working functions and outputs are reported
See this image and copyright information in PMC

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