CROCPOT is a repository and genome browser of data linking pairs of genomic loci for example from 3D chromatin interaction, single cell chromatin accessibility and CRISPRi screen assays. It builds on Locuszoom.js and enables the user to view a) ‘arc’ tracks linking pairs of genomic sites, b) genome-wide association data and c) gene definitions.
The key goal of CROCPOT is to help in prioritizing potential target genes of genetic variants associated with complex traits and disease.
This project is funded by the NIDDK, FNIH, and the AMP-T2D consortium.
CROCPOT Wiki https://www.crocpot.org/crocpot-doc/ for documentation Quick Start User Guide and uploading user's chromatin track
Locuszoom Wiki github.com/statgen/locuszoom/wiki for full documentation and API reference.
LocusZoom.js is choice of genome browser and base software for CROCPOT - a long range interaction browser. To install all necessary dependencies for a development environment, run:
$ npm install
We recommend using node.js v12 or greater to build the library and run tests.
Once complete run npm run build from the top of the application directory to run all tests and build the LocusZoom library bundle.
This build process will also write sourcemaps, to help with debugging code even in production environments.
npm run test- Run unit tests (optional:npm run test:coverageto output a code coverage report)npm run dev- Automatically rebuild the library whenever code changes (development mode)npm run build- Run tests, and if they pass, build the library for releasenpm run css- Rebuild the CSS using SASSnpm run docs- Build the library documentation
LocusZoom uses Mocha for unit testing. Tests are located in the test subdirectory.
LocusZoom is also linted using
ESLint, the rules for which can be found in .eslintrc. This will run automatically as part of all new code commits, and during every build.
If you have questions or feedback please file an issue on the CROCPOT GitHub repository or post at the discussion forum referenced above.