Package: ADAPT 0.99.1

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_0.99.1.tar.gz
ADAPT_0.99.1.zip(r-4.5)ADAPT_0.99.1.zip(r-4.4)ADAPT_0.99.1.zip(r-4.3)

ADAPT_0.99.1.tar.gz(r-4.5-noble)ADAPT_0.99.1.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'))

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-0.99.1(bioc 3.20)

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

4.96 score 26 scripts 3 exports 75 dependencies

Last updated 2 months agofrom:5eb19743d7. Checks:OK: 5. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 09 2024
R-4.5-win-x86_64	OK	Oct 09 2024
R-4.5-linux-x86_64	OK	Oct 09 2024
R-4.4-win-x86_64	OK	Oct 09 2024
R-4.3-win-x86_64	OK	Oct 09 2024

Exports:adapt plot summary

Dependencies:ade4 ape askpass Biobase BiocGenerics biomformat Biostrings cli cluster codetools colorspace cpp11 crayon curl data.table digest fansi farver foreach GenomeInfoDb GenomeInfoDbData ggplot2 ggrepel glue gtable httr igraph IRanges isoband iterators jsonlite labeling lattice lifecycle magrittr MASS Matrix mgcv mime multtest munsell nlme openssl permute phyloseq pillar pixmap pkgconfig plyr R6 RColorBrewer Rcpp RcppArmadillo RcppParallel reshape2 rhdf5 rhdf5filters Rhdf5lib rlang S4Vectors scales sp stringi stringr survival sys tibble UCSC.utils utf8 vctrs vegan viridisLite withr XVector zlibbioc

ADAPT Tutorial

Rendered fromADAPT-manual.Rmdusingknitr::rmarkdownon Oct 09 2024.

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