bioc-issue-bot
commented
2 months ago Hi @mkbwang
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: ADAPT
Title: Analysis of Microbiome Differential Abundance by Pooling Tobit Models
Version: 0.99.0
Authors@R:
c(person(given="Mukai", family="Wang", email="wangmk@umich.edu", role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-1413-1904")),
person(given="Simon", family="Fontaine", email="simfont@umich.edu", role = "ctb"),
person(given="Hui", family="Jiang", email="jianghui@umich.edu", role="ctb"),
person(given="Gen", family="Li", email="ligen@umich.edu", role=c("aut", "ctb")))
Description: 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.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2
Imports:
Rcpp (>= 1.0.8),
RcppArmadillo (>= 0.10.8),
RcppParallel (>= 5.1.5),
phyloseq (>= 1.39.0),
methods,
stats,
ggplot2 (>= 3.4.1),
ggrepel (>= 0.9.1)
Suggests:
rmarkdown (>= 2.11),
knitr (>= 1.37),
testthat (>= 3.0.0)
Config/testthat/edition: 3
LinkingTo:
Rcpp,
RcppArmadillo,
RcppParallel
biocViews:
DifferentialExpression,
Microbiome,
Normalization,
Sequencing,
Metagenomics,
Software,
MultipleComparison
Depends:
R (>= 4.1.0)
LazyData: false
VignetteBuilder: knitr
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