Package: ADAPT 1.7.0

Mukai Wang

ADAPT: Analysis of Microbiome Differential Abundance by Pooling Tobit Models

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.

Authors:Mukai Wang [aut, cre], Simon Fontaine [ctb], Hui Jiang [ctb], Gen Li [aut, ctb]

ADAPT_1.7.0.tar.gz
ADAPT_1.7.0.zip(r-4.7)ADAPT_1.7.0.zip(r-4.6)ADAPT_1.7.0.zip(r-4.5)

ADAPT_1.7.0.tar.gz(r-4.7-arm64)ADAPT_1.7.0.tar.gz(r-4.7-x86_64)ADAPT_1.7.0.tar.gz(r-4.6-arm64)ADAPT_1.7.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
card.svg |card.png
ADAPT/json (API)
NEWS

# Install 'ADAPT' in R:
install.packages('ADAPT', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:
  • ecc_plaque - Plaque samples from early childhood dental caries studies
  • ecc_saliva - Saliva samples from early childhood dental caries studies

On BioConductor:ADAPT-1.7.0(bioc 3.24)ADAPT-1.6.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

differentialexpressionmicrobiomenormalizationsequencingmetagenomicssoftwaremultiplecomparisonopenblascpp

4.61 score 41 scripts 202 downloads 3 exports 59 dependencies

Last updated from:c76579fcac. Checks:1 NOTE, 8 OK, 5 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE196
linux-devel-arm64OK238
linux-devel-x86_64OK270
source / vignettesOK274
linux-release-arm64OK238
linux-release-x86_64OK268
macos-release-arm64FAIL78
macos-release-x86_64FAIL196
macos-oldrel-arm64FAIL105
macos-oldrel-x86_64FAIL200
windows-develOK255
windows-releaseOK242
windows-oldrelOK229
wasm-releaseFAIL137

Exports:adaptplotsummary

Dependencies:ade4apeBiobaseBiocGenericsbiomformatBiostringscliclustercodetoolscpp11crayondata.tabledigestfarverforeachgenericsggplot2ggrepelgluegtableigraphIRangesisobanditeratorsjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmgcvmulttestnlmepermutephyloseqpixmappkgconfigplyrR6RColorBrewerRcppRcppArmadilloRcppParallelreshape2rlangS4VectorsS7scalesSeqinfospstringistringrsurvivalvctrsveganviridisLitewithrXVector

ADAPT Tutorial

Rendered fromADAPT-manual.Rmdusingknitr::rmarkdownon May 20 2026.

Last update: 2024-08-21
Started: 2024-04-14