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: | 1.0.4 |
| Depends: | R (≥ 4.1.0) |
| 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, httpuv |
| Published: | 2025-01-25 |
| DOI: | 10.32614/CRAN.package.ComBatFamQC |
| 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 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_1.0.4.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): ComBatFamQC_1.0.4.tgz, r-oldrel (x86_64): not available |
| Old sources: | ComBatFamQC archive |
Linking:
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