nci-webtools-dceg-mosaic-tiler

A webtool cataloging mosaic chromosomal alterations (mCAs) and interactively examining frequently altered genomic regions

Getting Started

1. In the database folder, create a data folder which contains the PLCO_GSA_*.txt datasets
2. In the database folder, run node createDatabase.js script to create database.db
3. In the server folder, create an .env file based on .env.example
4. In the server/.env file, ensure that DATABASE_PATH refers to the location of database.db
5. In the server folder, run npm start
6. Navigate to http://localhost:9000/api/ping in the browser to verify the application is running

Example Query

fetch("/api/query/samples", {
  method: "post",
  headers: { "content-type": "application/json" },
  body: JSON.stringify({
    conditions: [
      ["dataset", "in", ["PLCO_GSA_blood_autosomal_mCAs", "PLCO_GSA_blood_mLOY"]],
      ["chromosome", "in", ["chr1", "chrX"]],
      ["computedGender", "M"],
      ["callRate", ">", 0.99],
      ["cf", ">", 0.1],
    ],
  }),
}).then(async (e) => console.log(await e.json()));