benchdamic

DOI: 10.18129/B9.bioc.benchdamic  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see benchdamic.

Benchmark of differential abundance methods on microbiome data

Bioconductor version: 3.17

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>

Installation

To install this package, start R (version "4.3") and enter:

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

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")

 

HTML	R Script	Intro
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, Metagenomics, Microbiome, MultipleComparison, Normalization, Preprocessing, Software
Version	1.6.4
In Bioconductor since	BioC 3.14 (R-4.1) (2 years)
License	Artistic-2.0
Depends	R (>= 4.2.0)
Imports	stats, stats4, utils, methods, phyloseq, TreeSummarizedExperiment, BiocParallel, zinbwave, edgeR, DESeq2, limma, ALDEx2, SummarizedExperiment, MAST, Seurat, ANCOMBC, lme4, NOISeq, dearseq, MicrobiomeStat, Maaslin2, GUniFrac, metagenomeSeq, corncob, MGLM, ggplot2, RColorBrewer, plyr, reshape2, ggdendro, ggridges, graphics, cowplot, tidytext
LinkingTo
Suggests	knitr, rmarkdown, kableExtra, BiocStyle, magick, SPsimSeq, testthat
SystemRequirements
Enhances
URL
BugReports	https://github.com/mcalgaro93/benchdamic/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	benchdamic_1.6.4.tar.gz
Windows Binary	benchdamic_1.6.4.zip
macOS Binary (x86_64)
macOS Binary (arm64)	benchdamic_1.6.4.tgz
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/
Package Downloads Report	Download Stats