dar

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

Differential Abundance Analysis by Consensus

Bioconductor version: Development (3.21)

Differential abundance testing in microbiome data challenges both parametric and non-parametric statistical methods, due to its sparsity, high variability and compositional nature. Microbiome-specific statistical methods often assume classical distribution models or take into account compositional specifics. These produce results that range within the specificity vs sensitivity space in such a way that type I and type II error that are difficult to ascertain in real microbiome data when a single method is used. Recently, a consensus approach based on multiple differential abundance (DA) methods was recently suggested in order to increase robustness. With dar, you can use dplyr-like pipeable sequences of DA methods and then apply different consensus strategies. In this way we can obtain more reliable results in a fast, consistent and reproducible way.

Author: Francesc Catala-Moll [aut, cre] (ORCID: )

Maintainer: Francesc Catala-Moll <fcatala at irsicaixa.es>

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

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("dar")

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

Documentation


Reference Manual	PDF

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Details

biocViews	Metagenomics, Microbiome, MultipleComparison, Normalization, Sequencing, Software
Version	1.3.0
In Bioconductor since	BioC 3.19 (R-4.4) (0.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.4.0)
Imports	cli, ComplexHeatmap, crayon, dplyr, generics, ggplot2, glue, gplots, heatmaply, magrittr, methods, mia, phyloseq, purrr, readr, rlang (>= 0.4.11), scales, stringr, tibble, tidyr, UpSetR, waldo
System Requirements
URL	https://github.com/MicrobialGenomics-IrsicaixaOrg/dar https://microbialgenomics-irsicaixaorg.github.io/dar/
Bug Reports	https://github.com/MicrobialGenomics-IrsicaixaOrg/dar/issues

Suggests	ALDEx2, ANCOMBC, apeglm, ashr, Biobase, corncob, covr, DESeq2, devtools, furrr, future, knitr, lefser, limma, Maaslin2, metagenomeSeq, microbiome, rmarkdown, roxygen2, roxyglobals, roxytest, rstatix, SummarizedExperiment, TreeSummarizedExperiment, testthat (>= 3.0.0)
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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/dar
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/dar
Package Short Url	https://bioconductor.org/packages/dar/
Package Downloads Report	Download Stats