Package: ANCOMBC
Type: Package
Title: Microbiome differential abudance and correlation analyses with
        bias correction
Version: 2.14.0
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: 2026-04-27
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, DescTools, Hmisc, MASS, Matrix, Rdpack, doParallel,
        doRNG, energy, foreach, gtools, lme4, lmerTest, multcomp,
        nloptr, parallel, utils, quadprog
Suggests: mia (>= 1.18.0), 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: 7.3.3
Depends: R (>= 4.5.0)
LazyData: false
Config/pak/sysreqs: cmake make libgsl0-dev libicu-dev libuv1-dev
        libssl-dev libx11-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 12:53:35 UTC
RemoteUrl: https://github.com/bioc/ANCOMBC
RemoteRef: RELEASE_3_23
RemoteSha: 82bfaa10d60f6787fd559d742ab634873427d1e3
NeedsCompilation: no
Packaged: 2026-04-29 18:20:47 UTC; root
Author: Huang Lin [cre, aut] (ORCID: <https://orcid.org/0000-0002-4892-7871>)
Maintainer: Huang Lin <huanglinfrederick@gmail.com>
Built: R 4.6.0; ; 2026-04-29 18:40:11 UTC; windows
