Package: ADAPT 1.1.0

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_1.1.0.tar.gz
ADAPT_1.1.0.zip(r-4.5)ADAPT_1.1.0.zip(r-4.4)ADAPT_1.1.0.zip(r-4.3)

ADAPT_1.1.0.tar.gz(r-4.5-noble)ADAPT_1.1.0.tar.gz(r-4.4-noble)
ADAPT.pdf |ADAPT.html✨
ADAPT/json (API)
NEWS

# Install 'ADAPT' in R:
install.packages('ADAPT', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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-1.1.0(bioc 3.21)ADAPT-1.0.0(bioc 3.20)

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

differentialexpressionmicrobiomenormalizationsequencingmetagenomicssoftwaremultiplecomparisonopenblascpp

4.81 score 26 scripts 3 exports 75 dependencies

Last updated 3 months agofrom:ec4beeaabb. Checks:5 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 16 2025
R-4.5-win-x86_64OKJan 16 2025
R-4.5-linux-x86_64OKJan 16 2025
R-4.4-win-x86_64OKJan 16 2025
R-4.3-win-x86_64OKJan 16 2025

Exports:adaptplotsummary

Dependencies:ade4apeaskpassBiobaseBiocGenericsbiomformatBiostringscliclustercodetoolscolorspacecpp11crayoncurldata.tabledigestfansifarverforeachgenericsGenomeInfoDbGenomeInfoDbDataggplot2ggrepelgluegtablehttrigraphIRangesisobanditeratorsjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemulttestmunsellnlmeopensslpermutephyloseqpillarpixmappkgconfigplyrR6RColorBrewerRcppRcppArmadilloRcppParallelreshape2rhdf5rhdf5filtersRhdf5librlangS4VectorsscalesspstringistringrsurvivalsystibbleUCSC.utilsutf8vctrsveganviridisLitewithrXVector

ADAPT Tutorial

Rendered fromADAPT-manual.Rmdusingknitr::rmarkdownon Jan 16 2025.

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