BRAINscape: A Comprehensive Multi-Omics Analysis Tool

Overview

BRAINscape is an R package designed for integrative multi-omics analysis, specifically developed for the MU-BRAIN dataset, a multiethnic RNAseq dataset. The package facilitates stratified eQTL mapping and Differential Expression Analysis, providing a user-friendly framework for researchers to explore genetic and transcriptomic associations.

Features

• eQTL Analysis: Supports cis and trans eQTL mapping.
• Differential Expression Analysis: Uses DESeq2 for robust transcriptomic profiling.
• Interactive Data Exploration: Shiny-based web interface for data visualization.
• Supports Ethnicity-Specific Analysis: Users can filter results by Hispanic and Non-Hispanic Whites (NHW) groups.
• Advanced Visualization:
  • Manhattan Plots for eQTL results.
  • Volcano Plots for Differential Expression Analysis.

Installation

1. Install the dependencies: shiny, ggplot2, CMplot, dplyr using install.packages(c("shiny", "ggplot2", "CMplot", "dplyr", "DT", "plotly", "ggrepel"))
2. To install BRAINscape, first download the source file from zenodo and then install it using the following command:

install.packages("BRAINscape_1.0.0.tar.gz", repo=NULL, type="source")

Usage

library(BRAINscape)
BRAINscape::launchApp()

Example Workflow

1. Load and Explore eQTL Data

Select Ethinicity : Hispanics or Non-Hispanic Whites (NHW)
Select Analysis Type: eQTL
Select eQTL Type: cis or trans
Adjust Nominal P-value Threshold

# Example: Parameter selection and visualization for eQTL analysis
analysis_type <- "eQTL"
ethnicities <- "Non-Hispanic Whites (NHW)"
eqtl_type <- "trans"
gene <- "COLGALT2"
p_threshold <- 0.05

# Results will display Manhattan plots and interactive tables

Note: Due to large data size, the trans-eQTL data will take some time (around 10-15 secs) to load and reflect in the Shiny GUI.

2. Load and Explore Differential Expression Analysis Results

Select Ethinicity : Hispanics or Non-Hispanic Whites (NHW) or MU-BRAIN
Select Analysis Type: Differential Gene Expression
Adjust Cutoff for p-value (adjusted), BaseMean, and Log2FoldChange

# Example: Parameter selection and visualization for eQTL analysis
analysis_type <- "Differential Expression Analysis"
ethnicities <- "MUBRAIN"
adjusted_p_threshold <- 0.05

# Results will display volcano plot and interactive tables

3. Load and Explore GWAS Analysis Results

Select Ethinicity : Hispanics or Non-Hispanic Whites (NHW)
Select Analysis Type: GWAS
Adjust Nominal P-value Threshold

# Example: Parameter selection and visualization for eQTL analysis
analysis_type <- "GWAS"
ethnicities <- "Non-Hispanic Whites (NHW)"
p_threshold <- 0.05

# Results will display volcano plot and interactive tables

Data Sources

• The BRAINscape package does not include raw data due to data sharing constraints.

Citation

If you use BRAINscape for your research, please cite:

Yang, Z., Cieza, B., Reyes-Dumeyer, D., Lee, A., Ma, Y., Yilmaz, E., Lantigua, R., Miller, G.W., Brown, L.M., Honig, L. and Ciener, B., 2024. MU-BRAIN: MUltiethnic Brain Rna-seq for Alzheimer INitiative. bioRxiv, pp.2024-02.

Ruhela, V., Basilio Cieza Huaman, Zikun Yang, & Giuseppe Tosto. (2025). BRAINscape (1.0.0). Genetics and Genomics (Zenodo). https://doi.org/10.5281/zenodo.17831756

Contributing

We welcome contributions! To contribute:

1. Fork the repository.
2. Make improvements.
3. Submit a pull request.

Support

For issues and feature requests, please open a ticket on GitHub Issues.

License

This package is licensed under the Apache License. See LICENSE for details.

---

BRAINscape: Unlocking the Genetics of the Brain.