CRAVE

Contrasts-based Resource for Analysis, Visualisation, and Exploration

Abstract

CRAVE enables exploration of single contrasts between a pair of conditions in a biological experiment as well as analysis of trends across contrasts.

Deployment

CRAVE can be deployed as a Docker container or natively in Rshiny.

Docker Compose (recommended)

Clone this repo and navigate into it.

git clone https://github.com/SimonLammmm/crave.git
cd crave

Run CRAVE with Docker Compose

docker compose up -d

A preview of CRAVE is now accessible at http://localhost:8080.

Customise CRAVE by copying the shiny-server/config.example.R file as config.R and editing it. Update the docker-compose.yml file with any additional bind mounts you need.

Docker

Clone this repo and navigate into it.

git clone https://github.com/SimonLammmm/crave.git
cd crave

Build the Docker image.

cd docker
docker build -t crave:latest .

Run CRAVE with Docker

docker run --rm crave:latest -v "./shiny-server/config.example.R:/app/config.R" -v "./example-dataset/data/:/data/dataset-1/" -p 8080:3838

A preview of CRAVE is now accessible at http://localhost:8080.

Customise CRAVE by copying the shiny-server/config.example.R file as config.R and editing it. At runtime, bind mount that instead of config.example.R. Adjust the command with any additional bind mounts you need.

Rshiny

Run in native Rshiny on your local machine. Clone this repo and navigate into it.

git clone https://github.com/SimonLammmm/crave.git
cd crave

Copy the shiny-server/config.example.R file as shiny-server/config.R.

cp shiny-server/config.example.R shiny-server/config.R

Install dependencies found in the shiny-server/app.R script in the usual way for your system and then run Rshiny.

Rscript shiny-server/app.R

A preview of CRAVE is now accessible at http://localhost:8080.

Customise CRAVE by editing the shiny-server/config.R file.