ADAPT
This is the development version of ADAPT; for the stable release version, see ADAPT.
Analysis of Microbiome Differential Abundance by Pooling Tobit Models
Bioconductor version: Development (3.24)
ADAPT carries out differential abundance analysis for microbiome metagenomics data in phyloseq format. It has two innovations. One is to treat zero counts as left censored and use Tobit models for log count ratios. The other is an innovative way to find non-differentially abundant taxa as reference, then use the reference taxa to find the differentially abundant ones.
Author: Mukai Wang [aut, cre]
, Simon Fontaine [ctb], Hui Jiang [ctb], Gen Li [aut, ctb]
Maintainer: Mukai Wang <wangmk at umich.edu>
citation("ADAPT")):
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("ADAPT")
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("ADAPT")| ADAPT Tutorial | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, Metagenomics, Microbiome, MultipleComparison, Normalization, Sequencing, Software |
| Version | 1.7.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (2 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.1.0) |
| Imports | Rcpp (>= 1.0.8), RcppArmadillo (>= 0.10.8), RcppParallel (>= 5.1.5), phyloseq(>= 1.39.0), methods, stats, ggplot2 (>= 3.4.1), ggrepel (>= 0.9.1) |
| System Requirements | |
| URL |
See More
| Suggests | rmarkdown (>= 2.11), knitr (>= 1.37), testthat (>= 3.0.0) |
| Linking To | Rcpp, RcppArmadillo, RcppParallel |
| 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 | ADAPT_1.7.0.tar.gz |
| Windows Binary (x86_64) | ADAPT_1.7.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/ADAPT |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ADAPT |
| Bioc Package Browser | https://code.bioconductor.org/browse/ADAPT/ |
| Package Short Url | https://bioconductor.org/packages/ADAPT/ |
| Package Downloads Report | Download Stats |