Gene Enrichment with BRAD

BRAD Enrichment is a command-line tool to generate a report for gene enrichment analysis based on a gene set and targeted literature database. The tool uses a BRAD Agent to identify the contextual significance of enrichment terms and databases based upon custom a custom literature database. This repository contains command line tools brad-builddb and brad-enrichment for building literature databases and generating reports.

Quickstart

Run the following commands to install this tool:

pip install brad-enrichment
brad-builddb --help
brad-enrichment --help

See below for detailed list on installing this code.

Installation

To install BRAD Enrichment, activate your conda environment from the BRAD repository and install the following two packages:

conda activate BRAD
pip install BRAD-Agent
pip install brad-enrichment

Usage

Gene Enrichment Analysis

To perform gene enrichment analysis, use the following command:

brad-enrichment <gene_string> [OPTIONS]

Arguments

• <gene_string>: A string containing gene names separated by spaces or commas.

Options

• --databases, -d: List of databases to use for enrichment (default: KEGG, GO, PanglaoDB).
• --threshold-p-value, -p: P-value threshold for enrichment results (default: 0.05).
• --minimum-enrichment-terms, -min: Minimum number of enrichment terms to report (default: 3).
• --maximum-enrichment-terms, -max: Maximum number of enrichment terms to report (default: 10).
• --literature-database, -l: Path to the literature database (default: ../databases/enrichment_database).
• --output, -o: Output file name for results (default: enrichment_results.xlsx).
• --query, -q: Custom query for enrichment analysis (default: standard query).
• --verbose, -v: Enable verbose mode for debugging and logging.

Example Usage

brad-enrichment "TP53, MYC, EGFR" -d KEGG_2021_Human -p 0.01 -o my_results.xlsx

Building an Enrichment Literature Database

To build an enrichment literature database, use the following command:

brad-builddb [OPTIONS]

Options

• --documents-directory, -d: Path to the directory containing document files (default: documents).
• --database-directory, -D: Path to the directory where the database should be stored (default: databases).
• --database-name, -n: Name of the database to be created (default: enrichment_database).
• --text-size, -s: Size of text chunks for processing (default: 700).
• --text-overlap, -o: Number of overlapping characters between chunks (default: 100).
• --verbose, -v: Enable verbose output.

Example Usage

brad-builddb -d /path/to/documents -D /path/to/databases -n my_database -s 500 -o 50 -v

Development Setup

If you wish to contribute or modify the tool, follow these steps:

git clone https://github.com/Jpickard1/BRAD-Enrichment.git
cd BRAD-Enrichment
pip install -e .

Citation

If you use this tool in your research, please cite or paper Language Model Powered Digital Biology with BRAD as:

@article{pickard2024language,
  title={Language Model Powered Digital Biology with BRAD},
  author={Pickard, Joshua and Prakash, Ram and Choi, Marc Andrew and Oliven, Natalie and
          Stansbury, Cooper and Cwycyshyn, Jillian
          and Gorodetsky, Alex and Velasquez, Alvaro and Rajapakse, Indika},
  journal={arXiv preprint arXiv:2409.02864},
  url={https://arxiv.org/abs/2409.02864},
  year={2024}
}