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benchdamic

This is the development version of benchdamic; for the stable release version, see benchdamic.

Benchmark of differential abundance methods on microbiome data


Bioconductor version: Development (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 gmail.com>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("benchdamic")

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

Documentation

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

browseVignettes("benchdamic")
Intro HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, Metagenomics, Microbiome, MultipleComparison, Normalization, Preprocessing, Software
Version 1.9.1
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, 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
URL
Bug Reports https://github.com/mcalgaro93/benchdamic/issues
See More
Suggests knitr, rmarkdown, kableExtra, BiocStyle, magick, SPsimSeq, testthat
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Package Archives

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

Source Package benchdamic_1.9.1.tar.gz
Windows Binary benchdamic_1.9.1.zip
macOS Binary (x86_64) benchdamic_1.9.1.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/benchdamic
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/benchdamic
Bioc Package Browser https://code.bioconductor.org/browse/benchdamic/
Package Short Url https://bioconductor.org/packages/benchdamic/
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