DESCRIPTION

Package: ComBatFamQC
Title: Comprehensive Batch Effect Diagnostics and Harmonization
Version: 1.0.4
Authors@R: c(
    person("Zheng", "Ren", email = "zren1422@gmail.com", role = c("aut", "cre", "cph"), comment = c(ORCID = "0009-0006-2430-4625")),
    person("Andrew", "Chen", email = "chen1764@gmail.com", role = c("aut", "cph"), comment = c(ORCID = "0000-0002-5027-6422")),
    person("Elizabeth", "Horwath", email = "elizabeth.horwath@pennmedicine.upenn.edu", role = c("ctb"), comment = c(ORCID = "0009-0009-1224-6984"))
    )
Description: Provides a comprehensive framework for batch effect diagnostics, harmonization, and post-harmonization downstream analysis. Features include interactive visualization tools, robust statistical tests, and a range of harmonization techniques. Additionally, 'ComBatFamQC' enables the creation of life-span age trend plots with estimated age-adjusted centiles and facilitates the generation of covariate-corrected residuals for analytical purposes. Methods for harmonization are based on approaches described in Johnson et al., (2007) <doi:10.1093/biostatistics/kxj037>, Beer et al., (2020) <doi:10.1016/j.neuroimage.2020.117129>, Pomponio et al., (2020) <doi:10.1016/j.neuroimage.2019.116450>, and Chen et al., (2021) <doi:10.1002/hbm.25688>.
License: MIT + file LICENSE
URL: https://github.com/Zheng206/ComBatFamQC, https://zheng206.github.io/ComBatQC-Web/
BugReports: https://github.com/Zheng206/ComBatFamQC/issues
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Imports: 
    tidyr,
    dplyr,
    magrittr,
    ggplot2,
    DT,
    shiny,
    car,
    broom,
    pbkrtest,
    parallel,
    Rtsne,
    MDMR,
    gamlss,
    lme4,
    mgcv,
    bslib,
    shinydashboard,
    methods,
    gamlss.dist,
    invgamma,
    openxlsx
Depends: 
    R (>= 4.1.0)
LazyData: true
Suggests: 
    knitr,
    rmarkdown,
    devtools,
    testthat (>= 3.0.0),
    remotes,
    shinytest2,
    plotly,
    quarto,
    spelling,
    httpuv
VignetteBuilder: knitr
Config/testthat/edition: 3
Language: en-US