earmingol/singlecell-ccc repository overview

⁠singlecell-ccc

This is a Docker Image for running downstream single-cell RNA-seq analyses and evaluating cell-cell communication using jupyter notebooks.

Contains:

• Anaconda & Jupyter
• Python 3.8.8
• scanpy⁠
• cell2cell⁠
• R 4.0.3
• Seurat⁠
• SeuratDisk⁠
• Harmony⁠
• CellChat⁠

⁠Installation

1. Install docker following these instructions https://docs.docker.com/install/⁠

2. Pull the latest image from DockerHub with docker pull earmingol/singlecell-ccc

⁠Running the docker image

This docker image can be run with the following command. You should mount a local path so that your notebooks can be saved outside the Docker container.

docker run --rm -p 8888:8888 -v [local path]:/home/jovyan/work earmingol/singlecell-ccc:latest

You will then access the notebook with this URL:

http://127.0.0.1:8888/?token=[your token]

You can get the token from the console output from the docker run command.