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 (3.18)
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("benchdamic")):
Installation
To install this package, start R (version "4.3") 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 | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, Metagenomics, Microbiome, MultipleComparison, Normalization, Preprocessing, Software |
| Version | 1.7.4 |
| In Bioconductor since | BioC 3.14 (R-4.1) (2 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, lme4, NOISeq, dearseq, MicrobiomeStat, Maaslin2, GUniFrac, metagenomeSeq, corncob, MGLM, ggplot2, RColorBrewer, plyr, reshape2, ggdendro, ggridges, graphics, cowplot, tidytext |
| Linking To | |
| Suggests | knitr, rmarkdown, kableExtra, BiocStyle, magick, SPsimSeq, testthat |
| System Requirements | |
| Enhances | |
| URL | |
| Bug Reports | https://github.com/mcalgaro93/benchdamic/issues |
See More
| 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_1.7.4.tar.gz |
| Windows Binary | benchdamic_1.7.4.zip (64-bit only) |
| macOS Binary (x86_64) | benchdamic_1.7.4.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/ |
| Package Downloads Report | Download Stats |