https://github.com/imperial-genomics-facility/scanpy-notebook-image

A repository for keeping conda env and docker image file for running single cell analysis using scanpy
https://github.com/imperial-genomics-facility/scanpy-notebook-image

Last synced: 5 months ago
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A repository for keeping conda env and docker image file for running single cell analysis using scanpy

• Host: GitHub
• URL: https://github.com/imperial-genomics-facility/scanpy-notebook-image
• Owner: imperial-genomics-facility
• License: apache-2.0
• Created: 2019-12-18T13:14:12.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2024-03-06T16:32:28.000Z (over 1 year ago)
• Last Synced: 2025-04-19T10:28:22.806Z (6 months ago)
• Language: Jupyter Notebook
• Size: 10.4 MB
• Stars: 7
• Watchers: 2
• Forks: 3
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
[![DockerPulls](https://img.shields.io/docker/pulls/imperialgenomicsfacility/scanpy-notebook-image.svg)](https://registry.hub.docker.com/r/imperialgenomicsfacility/scanpy-notebook-image)

[![DockerStars](https://img.shields.io/docker/stars/imperialgenomicsfacility/scanpy-notebook-image.svg)](https://registry.hub.docker.com/r/imperialgenomicsfacility/scanpy-notebook-image)

[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/imperial-genomics-facility/scanpy-notebook-image/master?urlpath=lab)

[![nbviewer](https://img.shields.io/badge/launch-nbviewer-coral)](https://nbviewer.jupyter.org/github/imperial-genomics-facility/scanpy-notebook-image/tree/master/)

# 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](https://jupyterlab.readthedocs.io/en/latest/index.html)

* [Single cell analysis using Cellranger (10X genomics)](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)

* [Scanpy package for single cell data analysis](https://icb-scanpy.readthedocs-hosted.com/en/stable/)

## List of example notebooks:

* [Preprocessing and clustering 3k PBMCs from a Healthy Donor (10x Genomics) v0.0.5 :](https://nbviewer.jupyter.org/github/imperial-genomics-facility/scanpy-notebook-image/blob/master/examples/Clustering_3K_PBMCs_v0.0.5.ipynb) [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/imperial-genomics-facility/scanpy-notebook-image/master?urlpath=lab%2Ftree%2Fexamples%2FClustering_3K_PBMCs_v0.0.5.ipynb)

* [RNA Velocity Basics v 0.0.1:](https://nbviewer.jupyter.org/github/imperial-genomics-facility/scanpy-notebook-image/blob/master/examples/VelocityBasics_v0.0.1.ipynb) [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/imperial-genomics-facility/scanpy-notebook-image/master?urlpath=lab%2Ftree%2Fexamples%2FVelocityBasics_v0.0.1.ipynb)

## 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: 


  [![nbviewer](https://img.shields.io/badge/launch-nbviewer-coral)](https://nbviewer.jupyter.org/github/imperial-genomics-facility/scanpy-notebook-image/tree/master/)


## Run notebooks

### Using binder

Launce notebooks in binder for exploratory analysis: 


[![binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/imperial-genomics-facility/scanpy-notebook-image/master?urlpath=lab)


### Using Docker

* Install Docker following these instructions: [Docker Engine overview](https://docs.docker.com/install/)

* 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