Notebook container image for running single cell data analysis using scanpy

A repository for keeping conda env and docker image file for running single cell analysis using scanpy. Example notebooks are kept at examples dir and template notebooks are kept in templates dir.

Before using examples notebooks

List of prerequisites for using these example notebooks:

• JupyterLab Documentation
• Single cell analysis using Cellranger (10X genomics)
• Scanpy package for single cell data analysis

List of example notebooks:

• Preprocessing and clustering 3k PBMCs from a Healthy Donor (10x Genomics) v0.0.5 :

• RNA Velocity Basics v 0.0.1:

Installed packages

Please check the Dockerfile and environment.yml file for all the detail.

Explore notebooks

Explore the example notebooks from this repo in examples dir using nbviewer:

Run notebooks

Using binder

Launce notebooks in binder for exploratory analysis:

Using Docker

• Install Docker following these instructions: Docker Engine overview

• Use the following command to pull docker image from Docker hub

  • Pull the latest image

  docker pull imperialgenomicsfacility/scanpy-notebook-image
  

  • Pull a specific release

  docker pull imperialgenomicsfacility/scanpy-notebook-image:release-xyz
  

• Run notebook container in docker

docker run
  -p 8888:8888
  -v /path/:/tmp
  imperialgenomicsfacility/scanpy-notebook-image:tag

Using Singularity

• Build singularity image

singularity
  build
  scanpy-notebook-image.sif
  docker://imperialgenomicsfacility/scanpy-notebook-image

• Run jupyter notebook or nbconvert from singularity container

singularity
  run
  --bind /path:/tmp
  scanpy-notebook-image.sif
    jupyter nbconvert /tmp/notebook.ipynb --execute