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ComBatFamQC: Comprehensive Batch Effect Diagnostics and Harmonization

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>.

Version: 1.0.2
Depends: R (≥ 3.5.0)
Imports: tidyr, dplyr, magrittr, ggplot2, DT, shiny, car, broom, pbkrtest, parallel, Rtsne, MDMR, gamlss, lme4, mgcv, bslib, shinydashboard, methods, gamlss.dist, invgamma, openxlsx
Suggests: knitr, rmarkdown, devtools, testthat (≥ 3.0.0), remotes, shinytest2, plotly, quarto, spelling
Published: 2025-01-20
DOI: 10.32614/CRAN.package.ComBatFamQC
Author: Zheng Ren ORCID iD [aut, cre, cph], Andrew Chen ORCID iD [aut, cph], Elizabeth Horwath ORCID iD [ctb]
Maintainer: Zheng Ren <zren1422 at gmail.com>
BugReports: https://github.com/Zheng206/ComBatFamQC/issues
License: MIT + file LICENSE
URL: https://github.com/Zheng206/ComBatFamQC, https://zheng206.github.io/ComBatQC-Web/
NeedsCompilation: no
Language: en-US
Materials: README NEWS
CRAN checks: ComBatFamQC results

Documentation:

Reference manual: ComBatFamQC.pdf
Vignettes: ComBatFamQC_harmonization (source, R code)
Post-Harmonization (source, R code)

Downloads:

Package source: ComBatFamQC_1.0.2.tar.gz
Windows binaries: r-devel: ComBatFamQC_1.0.2.zip, r-release: ComBatFamQC_1.0.2.zip, r-oldrel: ComBatFamQC_1.0.2.zip
macOS binaries: r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): not available, r-oldrel (x86_64): not available

Linking:

Please use the canonical form https://CRAN.R-project.org/package=ComBatFamQC to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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