https://github.com/maayanlab/genesetcart
GeneSetCart is an interactive web-based platform that enables investigators to gather gene sets from various sources; augment these sets with gene-gene co-expression correlations and protein-protein interactions; perform set operations on these sets such as union, consensus, and intersection; and visualize and analyze these gene sets.
https://github.com/maayanlab/genesetcart
biomedical-data-science biomedical-informatics geneset-enrichment geneset-enrichment-analysis genesets genomics proteomics proteomics-data-analysis transcriptomics
Last synced: about 1 year ago
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GeneSetCart is an interactive web-based platform that enables investigators to gather gene sets from various sources; augment these sets with gene-gene co-expression correlations and protein-protein interactions; perform set operations on these sets such as union, consensus, and intersection; and visualize and analyze these gene sets.
- Host: GitHub
- URL: https://github.com/maayanlab/genesetcart
- Owner: MaayanLab
- License: gpl-3.0
- Created: 2024-01-29T17:40:43.000Z (over 2 years ago)
- Default Branch: master
- Last Pushed: 2025-02-10T03:20:58.000Z (over 1 year ago)
- Last Synced: 2025-02-10T03:23:57.818Z (over 1 year ago)
- Topics: biomedical-data-science, biomedical-informatics, geneset-enrichment, geneset-enrichment-analysis, genesets, genomics, proteomics, proteomics-data-analysis, transcriptomics
- Language: TypeScript
- Homepage: https://genesetcart.cfde.cloud/
- Size: 17.7 MB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# GeneSetCart
GeneSetCart is a platform for assembling, augmenting, combining, visualizing and analyzing gene sets: [https://genesetcart.cfde.cloud](https://genesetcart.cfde.cloud)
## Getting Started
```bash
# go to app (imagineset) directory
cd imagineset
# prepare .env file & review
cp .env.example .env
# start database
# (NOTE: If you're running another postgres database on your system, you should turn it off as the ports will conflict)
docker-compose up -d g2sg-postgres
# install node modules
npm i
# initialize prisma
npx prisma migrate deploy
# run dev server
npm run dev
```
Open [http://localhost:3000](http://localhost:3000) with your browser to see the platform.
## .env File Set Up
For the `NEXTAUTH_SECRET` value
Run
```
openssl rand -base64 32
```
Set NEXTAUTH_URL=http://localhost:3000
## Running the python backend
To run the python backend. Run the command:
```
gunicorn --workers 2 --timeout 600 --bind 0.0.0.0:8000 app:app
```
And set PYTHON_API_BASE='http://0.0.0.0:8000' in the .env file
## Provisioning the Database
To use the site, you have to populate your local database with gene and crossing pairs data. Firstly, make sure apply migrations to create the tables
```bash
# go to app (imagineset) directory
cd imagineset
npx prisma migrate deploy
```
and then run ingest script in database directory to add the data to these tables
```bash
# go to database directory (use the following commands if in imagineset directory):
cd ..
cd database
# download requirements
pip install -r requirements.txt
# prepare .env file containing DATABASE_URL
cp .env.example .env
# run ingest script
python3 ingest.py
```