ComBatFamQC

Streamline interactive batch effect diagnostics, harmonization, and post-harmonization downstream analysis to greatly simplify the data harmonization process and improve transparency and reproducibility.

https://github.com/zheng206/combatfamqc

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
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DOI references
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Scientific vocabulary similarity
Low similarity (13.2%) to scientific vocabulary

Keywords

diagnostic-tool harmonization rshinyapp

Last synced: 6 months ago · JSON representation

Repository

Basic Info

Host: GitHub
Owner: Zheng206
License: other
Language: R
Default Branch: main
Homepage:
Size: 244 MB

Statistics

Stars: 3
Watchers: 2
Forks: 4
Open Issues: 1
Releases: 0

Topics

diagnostic-tool harmonization rshinyapp

Created over 1 year ago · Last pushed 6 months ago

Metadata Files

Readme Changelog Contributing License Codemeta

README.md

ComBatFamQC

The ComBatFamQC package is a powerful tool designed to streamline interactive batch effect diagnostics, harmonization, and post-harmonization downstream analysis. This package is specifically tailored to provide both interactive qualitative visualization and statistical testing for batch effects diagnostics, as well as to offer various easily-used built-in harmonization techniques to facilitate a better harmonization process.

Additionally, the package provides life span age trends of brain structures and residual datasets, eliminating specific covariates' effects to better conduct post-harmonization downstream analysis. For the final delivery, the package offers interactive visualizations through R Shiny for batch effect diagnostics and age trend visualization. For users who wish to save a copy of the diagnostic report, the package also includes an option to generate a Quarto report (if Quarto is installed). Furthermore, it integrates the harmonization process and can provide a harmonized dataset, a fitted ComBat model, a residual dataset, a fitted regression model, and more.

To make the harmonization process more accessible to users from diverse backgrounds, two unified command-line interfaces have been developed for different stages of the processing pipeline (located in the inst folder):

CombatQC_CLI.R: Batch Effect Diagnostics & Harmonization Stage
- Offers interactive diagnostics for batch effects
- Export the batch effect diagnosis report
- Performs data harmonization to adjust for batch effects
post_CLI.R: Post-Harmonization Stage
- Visualizes age trends across brain structures over the lifespan
- Generates a residual dataset with unwanted covariate effects removed

Note: Detailed information and tutorials can be found: https://zheng206.github.io/ComBatQC-Web/

Diagram

ComBatFamQC Diagram

Package Features

The ComBatFamQC package offers the following five key functionalities:

Interactive Batch Effect Diagnostics & Harmonization

Batch Effect Diagnostics: ComBatFamQC provides two types of batch effect diagnostics methods for both individual batch effects and global batch effects: 1) Qualitative Visualization and 2) Statistical Testing. It simplifies the process of performing statistical analyses to detect potential batch effects and provides all relevant statistical test results for batch effect visualization and evaluation.
Harmonization: ComBatFamQC also provides four types of commonly used harmonization techniques, integrated through the ComBatFamily package developed by Dr. Andrew Chen, for users to consider. The four harmonization techniques include:
- Original ComBat (Johnson et al., 2007)
- Longitudinal ComBat (Beer et al., 2020)
- ComBat-GAM (Pomponio et al., 2020)
- CovBat (Chen et al., 2021)
Interactive Visualization through R Shiny: The ComBatFamQC package comes with an interactive visualization tool built on R Shiny, providing an intuitive user interface to explore and evaluate batch effects, as well as conduct interactive harmonization if needed. The output is organized into multiple tabs, which includes:
- Data Overview: Complete data overview and exploratory analysis
- Summary: Sample Size and Covariate Distribution
- Residual Plot: Additive and Multiplicative Batch Effect
- Diagnosis of Global Batch Effect: PCA, T-SNE and MDMR
- Diagnosis of Individual Batch Effect:
  - Statistical Tests for Additive Batch Effect: Kenward-Roger (liner mix model), ANOVA, Kruskal-Wallis
  - Statistical Tests for Multiplicative Batch Effect: Fligner-Killeen, Levene's Test, Bartlett's Test
- Harmonization Interactive Harmonization if needed

Post-Harmonization Downstream Analysis

Age Trajectory \ Generate age trend of each brain structure (ROI), adjusting sex and ICV. Customized centiles are enabled as well.
- Age Trend Plots
- Age Trend Table
Residual Generation \ Generate residual data set, removing specific covariates' effetcs.

Installation

CRAN

{r} install.packages("ComBatFamQC")

GitHub

The GitHub build is one release ahead of CRAN and includes out-of-sample harmonization for CovBat.

```{r} if (!require("devtools", quietly = TRUE)) { install.packages("devtools")
}

library(devtools)

devtools::installgithub("Zheng206/ComBatFamQC", buildvignettes = TRUE) ```

Tutorial

{r} vignette("ComBatQC") vignette("Post-Harmonization")

Command-line Interface

```{bash} RSCRIPT=${RSCRIPT:-$(command -v Rscript)} combatqccli="$($RSCRIPT -e 'cat(system.file("combatQCCLI.R", package="ComBatFamQC"))')" postcli="$($RSCRIPT -e 'cat(system.file("postCLI.R", package="ComBatFamQC"))')"

Rscript $combatqccli -h Rscript $postcli -h ```

Owner

Name: Zheng Ren
Login: Zheng206
Kind: user

Repositories: 1
Profile: https://github.com/Zheng206

CodeMeta (codemeta.json)

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GitHub Events

Total

Watch event: 2
Member event: 2
Push event: 225
Public event: 1
Fork event: 3
Create event: 1

Last Year

Watch event: 2
Member event: 2
Push event: 225
Public event: 1
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Packages

Total packages: 1
Total downloads:
- cran 208 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 4
Total maintainers: 1

cran.r-project.org: ComBatFamQC

Comprehensive Batch Effect Diagnostics and Harmonization

Homepage: https://github.com/Zheng206/ComBatFamQC
Documentation: http://cran.r-project.org/web/packages/ComBatFamQC/ComBatFamQC.pdf
License: MIT + file LICENSE
Latest release: 1.0.6
published 11 months ago

Versions: 4
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 208 Last month

Rankings

Dependent packages count: 27.4%

Dependent repos count: 33.8%

Average: 49.4%

Downloads: 86.9%

Maintainers (1)

zren1422@gmail.com

Last synced: 6 months ago

Dependencies

DESCRIPTION cran

R >= 3.5.0 depends
ComBatFamily * imports
DT * imports
MDMR * imports
Rtsne * imports
broom * imports
bsicons * imports
bslib * imports
car * imports
dplyr * imports
gamlss * imports
gamlss.dist * imports
ggplot2 * imports
invgamma * imports
lme4 * imports
methods * imports
mgcv * imports
parallel * imports
pbkrtest * imports
shiny * imports
shinydashboard * imports
tidyr * imports
tidyverse * imports
devtools * suggests
knitr * suggests
remotes * suggests
rmarkdown * suggests
testthat * suggests

.github/workflows/R-CMD-check.yaml actions

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r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

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jgehrcke/github-repo-stats RELEASE composite

.github/workflows/test-coverage.yaml actions

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actions/upload-artifact v4 composite
codecov/codecov-action v4 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

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ComBatFamQC

Science Score: 26.0%

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