Ketamine project

scRNA-seq analyses

Structure

ketamine_reproducibility
|-- README.md
|   
|-- docker
|   |-- Dockerfile
|   \-- python-packages.txt
\-- notebooks
    |-- 01-qc_preprocessing.ipynb
    |-- 02-annotation.ipynb
    |-- 03-differential_testing.ipynb
    |-- 04-figures.ipynb
    \-- gini.py

Installation

We provide a Dockerfile with all the packages required to run the analyses. To build the Docker image use the command:

docker build docker -t ketamine:final

After the image is compiled, you can run it interactively using:

docker run --interactive --tty --name ketamine --publish 8888:8888 --volume $HOME:/root/host_home --workdir /root ketamine:final  /bin/bash

This will start a container, in order to start a JupyterLab session use the alias:

jl

License

• MIT license