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 (3.21)

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] (ORCID: ), Chiara Romualdi [aut] (ORCID: ), Davide Risso [aut] (ORCID: ), Nicola Vitulo [aut] (ORCID: )

Maintainer: Matteo Calgaro <mcalgaro93 at gmail.com>

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

Installation

To install this package, start R (version "4.5") 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


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, Metagenomics, Microbiome, MultipleComparison, Normalization, Preprocessing, Software
Version	1.13.0
In Bioconductor since	BioC 3.14 (R-4.1) (3 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
URL
Bug Reports	https://github.com/mcalgaro93/benchdamic/issues

Suggests	knitr, rmarkdown, kableExtra, BiocStyle, magick, SPsimSeq, testthat
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Build Report	Build Report

Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
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
Package Short Url	https://bioconductor.org/packages/benchdamic/
Package Downloads Report	Download Stats