Package: ComBatFamQC 1.0.4

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_1.0.4.tar.gz
ComBatFamQC_1.0.4.zip(r-4.5)ComBatFamQC_1.0.4.zip(r-4.4)ComBatFamQC_1.0.4.zip(r-4.3)
ComBatFamQC_1.0.4.tgz(r-4.5-any)ComBatFamQC_1.0.4.tgz(r-4.4-any)ComBatFamQC_1.0.4.tgz(r-4.3-any)
ComBatFamQC_1.0.4.tar.gz(r-4.5-noble)ComBatFamQC_1.0.4.tar.gz(r-4.4-noble)
ComBatFamQC_1.0.4.tgz(r-4.4-emscripten)ComBatFamQC_1.0.4.tgz(r-4.3-emscripten)
ComBatFamQC.pdf |ComBatFamQC.html
ComBatFamQC/json (API)
NEWS

# 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

5.35 score 2 stars 16 scripts 558 downloads 23 exports 106 dependencies

Last updated 2 months agofrom:38fbcb9299. Checks:1 OK, 7 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 24 2025
R-4.5-winNOTEFeb 24 2025
R-4.5-macNOTEFeb 24 2025
R-4.5-linuxNOTEFeb 24 2025
R-4.4-winNOTEFeb 24 2025
R-4.4-macNOTEFeb 24 2025
R-4.3-winNOTEFeb 24 2025
R-4.3-macNOTEFeb 24 2025

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:abindbackportsbase64encbootbroombslibcachemcarcarDataclicolorspacecommonmarkCompQuadFormcowplotcpp11crayoncrosstalkDerivdigestdoBydplyrDTevaluatefansifarverfastmapfontawesomeFormulafsgamlssgamlss.datagamlss.distgenericsggplot2gluegtablehighrhtmltoolshtmlwidgetshttpuvinvgammaisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelme4magrittrMASSMatrixMatrixModelsMDMRmemoisemgcvmicrobenchmarkmimeminqamodelrmunsellnlmenloptrnnetnumDerivopenxlsxpbkrtestpillarpkgconfigpromisespurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppEigenRdpackreformulasrlangrmarkdownRtsnesassscalesshinyshinydashboardsourcetoolsSparseMstringistringrsurvivaltibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunxtableyamlzip

ComBatQC

Rendered fromComBatQC.Rmdusingknitr::rmarkdownon Feb 24 2025.

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

Post-Harmonization Downstream Analysis

Rendered fromPost-Harmonization.Rmdusingknitr::rmarkdownon Feb 24 2025.

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