Package: ComBatFamQC 1.0.6

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>.

Authors:Zheng Ren [aut, cre, cph], Andrew Chen [aut, cph], Elizabeth Horwath [ctb]

ComBatFamQC_1.0.6.tar.gz
ComBatFamQC_1.0.6.zip(r-4.7-any)ComBatFamQC_1.0.6.zip(r-4.6-any)ComBatFamQC_1.0.6.zip(r-4.5-any)
ComBatFamQC_1.0.6.tgz(r-4.6-any)ComBatFamQC_1.0.6.tgz(r-4.5-any)
ComBatFamQC_1.0.6.tar.gz(r-4.7-any)ComBatFamQC_1.0.6.tar.gz(r-4.6-any)
ComBatFamQC_1.0.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ComBatFamQC/json (API)

# Install 'ComBatFamQC' in R:
install.packages('ComBatFamQC', repos = c('https://zheng206.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/zheng206/combatfamqc/issues

Datasets:
  • adni - Harmonization Data
  • age_df - Age Trajectory Data

On CRAN:

Conda:

diagnostic-toolharmonizationrshinyapp

5.06 score 5 stars 23 scripts 371 downloads 23 exports 111 dependencies

Last updated from:a77ee72bf2. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develNOTE262
source / vignettesOK197
linux-releaseNOTE237
macos-releaseNOTE315
macos-oldrelNOTE279
windows-develNOTE228
windows-releaseNOTE217
windows-oldrelNOTE192
wasm-releaseOK134

Exports:.biweight_midvarage_list_genage_saveage_shinyage_table_genage_trend_plotcombat_harmcombat_plot_gencombat_table_gencomfamcomfam_shinycovfamcus_result_gencustomize_percentiledata_prepdiag_saveeb_checkform_gengetQuantileRefactoredinteraction_genmodel_genresidual_genvisual_prep

Dependencies:abindbackportsbase64encbootbroombslibcachemcarcarDataclicolorspacecommonmarkCompQuadFormcowplotcpp11crosstalkDerivdigestdoBydplyrDTevaluatefarverfastmapfontawesomeforecastFormulafracdifffsgamlssgamlss.datagamlss.distgenericsggplot2gluegtablehighrhtmltoolshtmlwidgetshttpuvinvgammaisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelme4lmtestmagrittrMASSMatrixMatrixModelsMDMRmemoisemgcvmimeminqamodelrnlmenloptrnnetnumDerivopenxlsxotelpbkrtestpillarpkgconfigpromisespurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrlangrmarkdownRtsneS7sassscalesshinyshinydashboardsourcetoolsSparseMstringistringrsurvivaltibbletidyrtidyselecttimeDatetinytexurcautf8vctrsviridisLitewithrxfunxtableyamlzipzoo

ComBatQC
Introduction | Set up | Interactive Batch Effect Diagnostics | Linear Regression Model | Generalized additive Model | Linear Mixed-Effects Model | Export Batch Effect Diagnosis Result | Harmonization Using default ComBatFamily Methods | First-time Harmonization | Original ComBat | Longitudinal ComBat | ComBat-GAM | CovBat | Out of Sample Harmonization | from ComBat Model | from Reference Data
Rendered fromComBatQC.Rmdusingknitr::rmarkdown

Last update: 2025-01-17
Started: 2024-10-27

Post-Harmonization Downstream Analysis
Introduction | Set up | Life Span Age Trend Visualization | Create a list of data sets for all ROIs | Create age trend estimation for all ROIs | Launch Shiny App for Visualization | Save Age Trend Table and GAMLSS Model | Residual Generation | Get harmonized data set | Generate residual data set | Generate residuals from scratch | Generate residuals from existing model
Rendered fromPost-Harmonization.Rmdusingknitr::rmarkdown

Last update: 2025-01-17
Started: 2024-10-27