Package: ComBatFamQC
Title: Comprehensive Batch Effect Diagnostics and Harmonization
Version: 1.0.6
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
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,
        plotly, quarto, spelling, systemfonts,
VignetteBuilder: knitr
Config/testthat/edition: 3
Language: en-US
NeedsCompilation: no
Packaged: 2025-03-23 19:14:43 UTC; zhengren
Author: Zheng Ren [aut, cre, cph] (<https://orcid.org/0009-0006-2430-4625>),
  Andrew Chen [aut, cph] (<https://orcid.org/0000-0002-5027-6422>),
  Elizabeth Horwath [ctb] (<https://orcid.org/0009-0009-1224-6984>)
Maintainer: Zheng Ren <zren1422@gmail.com>
Repository: CRAN
Date/Publication: 2025-03-24 00:50:06 UTC
Built: R 4.5.1; ; 2025-10-06 04:03:08 UTC; windows
