A web platform for exploring neuropsychiatric genetics data from the SSPsyGene consortium at UCSC. Integrates differential expression, perturbation screens, phenotype annotations, and curated databases into a searchable gene-centric interface.
Live site: https://psypheno.gi.ucsc.edu/
data/
datasets/ Per-dataset configs, data files, and preprocessing scripts
homology/ Gene homology mapping files (HGNC, MGI, ZFIN, Alliance)
db/ Generated SQLite database (not in git)
processing/ Python pipeline — loads datasets into SQLite (Click CLI)
web/ Next.js web application (React, TypeScript, better-sqlite3)
docs/ Documentation
| Document | Description |
|---|---|
| Adding Datasets | Step-by-step guide for data wranglers adding new datasets |
| Server Architecture | Production/dev/internal server instances and deployment |
| Local Development | Setting up and running the project locally |
# Install Python pipeline
conda create -n sspsygene python=3.13 && conda activate sspsygene
cd processing && pip install -e . && cd ..
# Set environment variables
export SSPSYGENE_DATA_DIR="$(pwd)/data"
export SSPSYGENE_CONFIG_JSON="processing/src/processing/config.json"
export SSPSYGENE_DATA_DB="$(pwd)/data/db/sspsygene.db"
# Build database and start web app
sspsygene load-db
cd web && npm install && npm run devSee docs/development.md for full setup instructions.