TCGA splice-junction analysis

SpliceRx

Interactive tools for exploring splice-junction data prepared with the prepTCGAdata R package — sashimi plots, cohort-level heatmaps, survival-group classification, and junction lookup, all in one app you run on your own machine.

View on GitHub Run it locally

This is a local-first research tool, not a hosted service. The app reads TCGA cohort files straight off the filesystem of the machine it runs on, so it works against your own prepared cohorts. Clone the repo and start it locally — it's a two-command setup, see below.

What's inside

DATA

Data

Point the app at a local directory of prepared TCGA cohort files — the one way any tab gets data in.

SJV

Sashimi plot

SCANVIS-style sashimi plot of splice-junction coverage for one sample or a sample group.

SJVC

NSJCG

Cohort-level heatmap, PCA and UMAP of novel-splice-junction-per-gene counts, with clinical variables layered on.

SJSurv

Survival groups

Cross-validated logistic regression classifying a Good / Poor survival label from a splice-junction feature matrix.

LOOKUP

SJ Lookup

Direct per-junction lookup against junction metadata.

Quick start

git clone https://github.com/agiusp/SpliceRx.git
cd SpliceRx/app/backend
python3 -m venv .venv && .venv/bin/pip install -r requirements.txt
.venv/bin/python -m uvicorn main:app --port 8000 --reload

# in a second terminal
cd SpliceRx/app/frontend
npm install && npm run dev   # open http://localhost:5173

See the full README for prerequisites, pointing the app at your own cohort data, and running the test suite.