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.

differentialexpressionmicrobiomenormalizationsequencingmetagenomicssoftwaremultiplecomparison

4.89 score 26 scripts 3 exports 76 dependencies

Last updated 23 days agofrom:ec4beeaabb. Checks:OK: 1 WARNING: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 17 2024
R-4.5-win-x86_64WARNINGNov 17 2024
R-4.5-linux-x86_64WARNINGNov 17 2024
R-4.4-win-x86_64WARNINGNov 17 2024
R-4.3-win-x86_64WARNINGNov 17 2024

Exports:adaptplotsummary

Dependencies:ade4apeaskpassBiobaseBiocGenericsbiomformatBiostringscliclustercodetoolscolorspacecpp11crayoncurldata.tabledigestfansifarverforeachgenericsGenomeInfoDbGenomeInfoDbDataggplot2ggrepelgluegtablehttrigraphIRangesisobanditeratorsjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemulttestmunsellnlmeopensslpermutephyloseqpillarpixmappkgconfigplyrR6RColorBrewerRcppRcppArmadilloRcppParallelreshape2rhdf5rhdf5filtersRhdf5librlangS4VectorsscalesspstringistringrsurvivalsystibbleUCSC.utilsutf8vctrsveganviridisLitewithrXVectorzlibbioc

ADAPT Tutorial

Rendered fromADAPT-manual.Rmdusingknitr::rmarkdownon Nov 17 2024.

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