Structural and Functional Characterization of G Protein-Coupled Receptors with Deep Mutational Scanning

Requisite code and data to reproduce Jones and Lubock et al. 2019.

Installation

Clone this repository

git clone  https://github.com/KosuriLab/b2-dms.git

Pull the image from docker hub

docker pull nlubock/b2-dms

Or build it from scratch

docker build -t b2-dms ./docker

Requirements

The processed data can be analyzed on any standard laptop with at least 16 GB of RAM. The raw sequencing data should be processed on a machine with at least 64 GB of RAM.

Usage

RStudio

The docker image relies on the Rocker Project to provide RStudio. To link this repository to the docker image run

docker run -d  -e PASSWORD=yourpassword -p 8787:8787 -p 8888:8888 -v /path/to/b2-dms:/home/rstudio/b2-dms nlubock/b2-dms

Then point your browser to localhost:8787 and use rstudio and yourpassword to log in

Jupyter

The docker image also supports Jupyter notebooks. To run one, drop into the image and start a notebook

docker ps
docker exec -it image_name /bin/bash
jupyter notebook --ip 0.0.0.0 --no-browser --allow-root

then point your browser to localhost:8888 to run it

Contributing

Pull requests are encouraged. For major changes, please open an issue first to discuss what you would like to change.

License

MIT