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✨
DESCRIPTION |NEWS
card.svg |card.png
ADAPT/json (API)

# 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.

differentialexpression microbiome normalization sequencing metagenomics software multiplecomparison openblas cpp

4.67 score 47 scripts 3 exports 59 dependencies

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

Target	Result	Time
bioc-checks	NOTE	197
linux-devel-arm64	OK	230
linux-devel-x86_64	OK	271
source / vignettes	OK	281
linux-release-arm64	OK	217
linux-release-x86_64	OK	314
macos-release-arm64	FAIL	79
macos-release-x86_64	FAIL	172
macos-oldrel-arm64	FAIL	85
macos-oldrel-x86_64	FAIL	285
windows-devel	OK	278
windows-release	OK	269
windows-oldrel	OK	230
wasm-release	FAIL	131

Exports:adapt plot summary

Dependencies:ade4 ape Biobase BiocGenerics biomformat Biostrings cli cluster codetools cpp11 crayon data.table digest farver foreach generics ggplot2 ggrepel glue gtable igraph IRanges isoband iterators jsonlite labeling lattice lifecycle magrittr MASS Matrix mgcv multtest nlme permute phyloseq pixmap pkgconfig plyr R6 RColorBrewer Rcpp RcppArmadillo RcppParallel reshape2 rlang S4Vectors S7 scales Seqinfo sp stringi stringr survival vctrs vegan viridisLite withr XVector

ADAPT Tutorial

Introduction | Main function adapt | Explore Analysis Results | Session Information and References

Rendered fromADAPT-manual.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
ADAPT	adapt
Differential abundance analysis result	DAresult-class
Plaque samples from early childhood dental caries studies	ecc_plaque
Saliva samples from early childhood dental caries studies	ecc_saliva
Plotting differential abundance analysis results	plot,DAresult,ANY-method
Summary of differential abundance analysis	summary,DAresult-method