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 (>= 4.4.0)
LazyData: false
Config/pak/sysreqs: cmake libgmp3-dev make libgsl0-dev libicu-dev
        libmpfr-dev libssl-dev libx11-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:02:01 UTC
RemoteUrl: https://github.com/bioc/ANCOMBC
RemoteRef: RELEASE_3_22
RemoteSha: 5ceba73f418b58d137f09694d41cab53b30116cc
NeedsCompilation: no
Packaged: 2025-11-11 12:55:56 UTC; root
Author: Huang Lin [cre, aut] (ORCID: <https://orcid.org/0000-0002-4892-7871>)
Maintainer: Huang Lin <huanglinfrederick@gmail.com>
Built: R 4.5.2; ; 2025-11-11 13:03:45 UTC; windows
