Package: ANCOMBC
Type: Package
Title: Microbiome differential abudance and correlation analyses with
        bias correction
Version: 2.12.0
Description: ANCOMBC is a package containing differential abundance (DA) and 
    correlation analyses for microbiome data. Specifically, the package includes 
    Analysis of Compositions of Microbiomes with Bias Correction 2 (ANCOM-BC2),
    Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC), and 
    Analysis of Composition of Microbiomes (ANCOM) for DA analysis, and Sparse 
    Estimation of Correlations among Microbiomes (SECOM) for correlation 
    analysis. Microbiome data are typically subject to two sources of biases: 
    unequal sampling fractions (sample-specific biases) and differential 
    sequencing efficiencies (taxon-specific biases). Methodologies included in 
    the ANCOMBC package are designed to correct these biases and construct 
    statistically consistent estimators.
Date: 2025-03-16
Authors@R: c(
    person(given = "Huang", 
           family = "Lin", 
           email = "huanglinfrederick@gmail.com", 
           role = c("cre", "aut"),
           comment = c(ORCID = "0000-0002-4892-7871")))
License: Artistic-2.0
Imports: stats, CVXR, DescTools, Hmisc, MASS, Matrix, Rdpack,
        doParallel, doRNG, energy, foreach, gtools, lme4, lmerTest,
        multcomp, nloptr, parallel, utils
Suggests: mia (>= 1.6.0), DT, S4Vectors, SingleCellExperiment,
        SummarizedExperiment, TreeSummarizedExperiment, dplyr, knitr,
        magrittr, microbiome, phyloseq, rmarkdown, testthat, tidyr,
        tidyverse
biocViews: DifferentialExpression, Microbiome, Normalization,
        Sequencing, Software
BugReports: https://github.com/FrederickHuangLin/ANCOMBC/issues
URL: https://github.com/FrederickHuangLin/ANCOMBC
VignetteBuilder: knitr
RdMacros: Rdpack
Encoding: UTF-8
RoxygenNote: 7.3.2
Depends: R (>= 4.5.0)
LazyData: false
git_url: https://git.bioconductor.org/packages/ANCOMBC
git_branch: RELEASE_3_22
git_last_commit: 5ceba73
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.22
Date/Publication: 2025-10-29
NeedsCompilation: no
Packaged: 2025-10-30 02:49:19 UTC; biocbuild
Author: Huang Lin [cre, aut] (ORCID: <https://orcid.org/0000-0002-4892-7871>)
Maintainer: Huang Lin <huanglinfrederick@gmail.com>
