Registration Open for Bioc2024 July 24-26


Benchmark of differential abundance methods on microbiome data

Bioconductor version: Release (3.19)

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.

Author: Matteo Calgaro [aut, cre] , Chiara Romualdi [aut] , Davide Risso [aut] , Nicola Vitulo [aut]

Maintainer: Matteo Calgaro <mcalgaro93 at>

Citation (from within R, enter citation("benchdamic")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Intro HTML R Script
Reference Manual PDF


biocViews DifferentialExpression, Metagenomics, Microbiome, MultipleComparison, Normalization, Preprocessing, Software
Version 1.10.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License Artistic-2.0
Depends R (>= 4.3.0)
Imports stats, stats4, utils, methods, phyloseq, TreeSummarizedExperiment, BiocParallel, zinbwave, edgeR, DESeq2, limma, ALDEx2, corncob, SummarizedExperiment, MAST, Seurat, ANCOMBC, mixOmics, lme4, NOISeq, dearseq, MicrobiomeStat, Maaslin2, GUniFrac, metagenomeSeq, MGLM, ggplot2, RColorBrewer, plyr, reshape2, ggdendro, ggridges, graphics, cowplot, grDevices, tidytext
System Requirements
Bug Reports
See More
Suggests knitr, rmarkdown, kableExtra, BiocStyle, magick, SPsimSeq, testthat
Linking To
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package benchdamic_1.10.0.tar.gz
Windows Binary
macOS Binary (x86_64) benchdamic_1.10.0.tgz
macOS Binary (arm64) benchdamic_1.10.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats