dar
This is the development version of dar; for the stable release version, see dar.
Differential Abundance Analysis by Consensus
DOI: 10.18129/B9.bioc.dar
Bioconductor version: Development (3.24)
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]
Maintainer: Francesc Catala-Moll <fcatala at irsicaixa.es>
citation("dar")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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, ComplexHeatmap, crayon, dplyr, generics, ggplot2, glue, gplots, heatmaply, magrittr, methods, mia, phyloseq, purrr, readr, rlang (>= 0.4.11), scales, stringr, tibble, tidyr, UpSetR |
| 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, ANCOMBC, apeglm, ashr, Biobase, corncob, covr, DESeq2, devtools, furrr, future, knitr, lefser, limma, maaslin3, microbiome, rmarkdown, roxygen2, roxyglobals, roxytest, rstatix, SummarizedExperiment, TreeSummarizedExperiment, testthat (>= 3.0.0), GenomeInfoDb, withr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/dar/ |
| Package Short Url | https://bioconductor.org/packages/dar/ |
| Package Downloads Report | Download Stats |