zh1peng / brainenrich

BrainEnrich: Revealing Biological Insights from Imaging-Derived Features through Transcriptomic Enrichment 🧠🧬

Aim of the Toolbox 🎯

BrainEnrich is an R package designed to facilitate the correlation of imaging-derived phenotypes with transcriptional profiles. This toolbox aims to provide researchers and clinicians with robust statistical tools to uncover molecular architectures associated with cognitive functions, brain development, and disorders.

Timeline of Development 🗓️

• Q4 2023: Initial conceptualization and development of core functions. 🛠️
• Q1 2024: Implementation of competitive null models and self-contained null models. 🧪
• Q1 2024: Testing with simulated datasets and refinement of statistical tests. 🔬
• Q2 2024: Beta release for community feedback and additional testing. 🔄
• Q3 2024: Incorporation of feedback and preparation for CRAN submission. ✍️
• Q4 2024: Submission to CRAN and publication of accompanying paper. 📰

Installation 💾

Please note that brainEnrich is currently in development and not yet available for installation.

Once available, it can be installed from GitHub via the devtools package:

# Install remotes if you haven't already
if (!requireNamespace("remotes", quietly = TRUE)) {
      install.packages("remotes")}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}
BiocManager::install("DOSE")
# Install brainEnrich from GitHub
remotes::install_github("zh1peng/BrainEnrich")

Usage 📖

Instructions on how to use the toolbox will be provided here, including example code.

To-Do List 📋

• Initialize the project 2023/11/04
• Finalize manuscript revision. 🔧
• Development of core functions🔧
• Create detailed vignettes for each major function. 📚
• Optimize performance for large datasets. ⚡
• Conduct extensive testing with real-world data. 🌏
• Develop a comprehensive test suite. ✅
• Set up continuous integration for automated testing. 🔄
• Prepare documentation for public release. 📄

Contributing 🤝

Versioning 🏷️

We use git for versioning. For the versions available, see the tags on this repository.

Authors 👩‍💻👨‍💻

• Zhipeng Cao @ Xuhui Mental Health Center, Shanghai - Initial work - zh1peng

License 📜

This project is licensed under the GNU Affero General Public (AGP) License - see the LICENSE.md file for details.

Acknowledgments 👏