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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