This is the development version of benchdamic; for the stable release version, see benchdamic.
Benchmark of differential abundance methods on microbiome dataBioconductor version: Development (3.22)
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: 0000-0002-3056-518X , Chiara Romualdi [aut] ORCID: 0000-0003-4792-9047 , Davide Risso [aut] ORCID: 0000-0001-8508-5012 , Nicola Vitulo [aut] ORCID: 0000-0002-9571-0747
Maintainer: Matteo Calgaro <mcalgaro93 at gmail.com>
Citation (from within R, entercitation("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 Details biocViews DifferentialExpression, Metagenomics, Microbiome, MultipleComparison, Normalization, Preprocessing, Software Version 1.15.2 In Bioconductor since BioC 3.14 (R-4.1) (3.5 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, microbiome, mixOmics, lme4, NOISeq, dearseq, MicrobiomeStat, Maaslin2, maaslin3, 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 Package ArchivesFollow 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 StatsRetroSearch is an open source project built by @garambo | Open a GitHub Issue
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