ExpressDiff

ExpressDiff is an HPC-oriented RNA-seq pipeline with a web UI. It provides a FastAPI backend that orchestrates SLURM stages and a React/TypeScript frontend for run creation, file upload, pipeline execution, and results viewing.

Start Here

• Documentation index: ExpressDiff/docs/INDEX.md:1
• End-user guide (UI): ExpressDiff/frontend/USER_GUIDE.md:1
• Quick reference: ExpressDiff/frontend/QUICK_REFERENCE.md:1
• Bundled demo dataset: ExpressDiff/docs/DEMO_DATASET.md:1

Quick Start (Users)

HPC module deployment (recommended)

salloc -A <your_account> -p standard -c 4 --mem=16G -t 02:00:00
module load expressdiff
ExpressDiff run

Default module-launcher ports:

• Backend: 51234
• Frontend: 51235

See ExpressDiff/docs/DEPLOYMENT_HPC.md:1.

Quick Start (Developers)

Run from source (local dev defaults)

cd ExpressDiff
python -m venv venv
source venv/bin/activate
pip install -r requirements.txt
uvicorn backend.api.main:app --reload --host 0.0.0.0 --port 8000

cd ExpressDiff/frontend
npm install
REACT_APP_API_URL=http://localhost:8000 npm start

Default dev ports:

• Backend: 8000
• Frontend: 3000

See ExpressDiff/docs/INSTALLATION.md:1.

Pipeline Overview

Stages (in order) are defined by SLURM templates in ExpressDiff/slurm_templates/qc_raw.slurm.template:1 and managed by the backend:

1. QC (raw): FastQC + MultiQC
2. Trim: Trimmomatic
3. QC (trimmed): FastQC + MultiQC
4. Align: STAR
5. Count: featureCounts
6. Differential expression: “DESeq2” stage implemented via PyDESeq2

Canonical stage reference: ExpressDiff/docs/PIPELINE.md:1.

Tools Used

• Bioinformatics tools: ExpressDiff/docs/TOOLS_BIOINFORMATICS.md:1
• Implementation tools (FastAPI/React/SLURM integration): ExpressDiff/docs/TOOLS_IMPLEMENTATION.md:1

Repository Layout

See ExpressDiff/REPOSITORY_ORGANIZATION.md:1 for a full tree; key directories:

• ExpressDiff/backend/ — FastAPI backend
• ExpressDiff/frontend/ — React frontend
• ExpressDiff/slurm_templates/ — SLURM job templates
• ExpressDiff/test_data_generators/ — scripts to generate small test/demo data

Support

Contact: vth3bk@virginia.edu