HumanBase documentation

This repository contains the documentation source files for HumanBase. These files are Sphinx docs written with reStructuredText.

Build Status

Check the Read the Docs build status and documentation: https://app.readthedocs.org/projects/humanbase/

The live documentation is available at: https://humanbase.readthedocs.io/

Preview Builds: Read the Docs can build documentation for pull requests, but this needs to be triggered. To preview your changes before merging:

1. Create a pull request from your branch to master
2. Go to https://app.readthedocs.org/projects/humanbase/ to trigger a build

Quick Start

Prerequisites

• Python 3.8 or higher
• pip (Python package installer)
• Make (for building documentation)

Local Development Setup

# Clone the repository
git clone https://github.com/aaronkw/humanbase-docs.git
cd humanbase-docs

# Create and activate a virtual environment
python3 -m venv venv
source venv/bin/activate

# Install dependencies
pip install -r docs/requirements.txt

Building Documentation Locally

# Navigate to the docs directory
cd docs

# Clean previous builds (optional)
make clean

# Build HTML documentation
make html

# View the documentation
open _build/html/index.html  # On macOS
# Or: python -m http.server -d _build/html 8000  # Then visit http://localhost:8000

Documentation Structure

The documentation is organized as follows:

• docs/ - Main documentation directory
  • index.rst - Main table of contents and entry point
  • conf.py - Sphinx configuration file
  • requirements.txt - Python dependencies for building docs
  • img/ - Images and diagrams used in documentation
  • Tool-specific documentation:
    • sei.rst - Sei/DeepSEA sequence-based predictions
    • beluga.rst - DeepSEA (Beluga) chromatin profile predictions
    • expecto.rst - ExPecto expression predictions
    • expectosc.rst - ExPectoSC variant effect predictions
    • netwas.rst - NetWAS network-based association studies
    • in-silico-mutagenesis.rst - In silico mutagenesis analysis
  • Network documentation:
    • functional-networks.rst - Functional gene networks
    • tissue-networks.rst - Tissue-specific networks
• .readthedocs.yaml - Read the Docs build configuration
• README.rst - This file