dar
This is the development version of dar; for the stable release version, see dar.
Differential Abundance Workflows for Microbiome Data
DOI: 10.18129/B9.bioc.dar
Bioconductor version: Development (3.24)
Provides a recipe-based interface for differential abundance analysis of microbiome data. A shared model specification defines covariates, contrasts, reference levels and taxonomic aggregation, with compatibility checks for each method. Pipeable workflows combine preprocessing, quality control and multiple differential abundance methods. Results can be inspected in a common format that preserves method-specific effect scales, visualized and compared. Recipes can be exported and imported using a versioned, non-executable format. Optional consensus rules summarize agreement across methods for each contrast and effect direction.
Author: Francesc Catala-Moll [aut, cre] 
Maintainer: Francesc Catala-Moll <fcatala at irsicaixa.es>
citation("dar")):Francesc Catala-Moll. dar: Differential Abundance Workflows for Microbiome Data. doi:10.18129/B9.bioc.dar, R package version 1.9.0, https://bioconductor.org/packages/dar.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("dar")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("dar")| Data Import | HTML | R Script |
| Filtering and Subsetting | HTML | R Script |
| Introduction to dar | HTML | R Script |
| Reproducibility in Microbiome Data Analysis | HTML | R Script |
| Workflow with real data | HTML | R Script |
| Workflow with real data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Metagenomics, Microbiome, MultipleComparison, Normalization, Sequencing, Software |
| Version | 1.9.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | checkmate, cli, crayon, dplyr, generics, ggplot2, glue, jsonlite, magrittr, methods, mia, phyloseq, purrr, reformulas, rlang (>= 0.4.11), scales, stringr, tibble, tidyr, withr |
| System Requirements | |
| URL | https://github.com/MicrobialGenomics-IrsicaixaOrg/dar https://microbialgenomics-irsicaixaorg.github.io/dar/ |
| Bug Reports | https://github.com/MicrobialGenomics-IrsicaixaOrg/dar/issues |
See More
| Suggests | ALDEx2, ALDEx3 (>= 1.3.1), ANCOMBC, apeglm, ashr, Biobase, corncob, ComplexHeatmap, covr, DESeq2, devtools, furrr, future, gplots, heatmaply, knitr, lefser, limma, maaslin3, microbiome, MicrobiomeStat, radEmu (>= 2.3.2.0), readr, rmarkdown, roxygen2, roxyglobals, roxytest, SummarizedExperiment, TreeSummarizedExperiment, UpSetR, testthat (>= 3.0.0), GenomeInfoDb |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | dar_1.9.0.tar.gz |
| Windows Binary (x86_64) | dar_1.9.0.zip |
| macOS Binary (big-sur-x86_64) | dar_1.9.0.tgz |
| macOS Binary (sonoma-arm64) | dar_1.9.0.tgz |
| 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 |