Giotto Tutorial Binder

🔴 Note: Please read the instructions below before launching the Binder as there is some important information about how Binder works and how you can use it optimally. 🔴

Table of contents

1. What is Binder?: A brief overview on what Binder is and how it works in this context

2. Examples and data used: Links to the tutorials and data available on the website

3. Instructions: Steps for usage

4. Directory: Easy navigation to the files in this repository

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What is Binder?

Binder utilizes JupyterHub, repo2docker, and BinderHub to create a docker image built off of a GitHub repository.

By clicking , the environment will automatically be created and you’ll be able to run the jupyter notebooks in this repository on Binder’s servers.

Things to note

• The first time you build this Binder, it may take while. For some more information on why your session might be taking longer, please refer to this link.

  • Below are some commmon messages you might see. They are normal! Just give the Binder some more time to load.

    Your session is taking longer than usual to start! Check the log messages below to see what is happening.

    Launch attempt 1 failed, retrying... Launch attempt 2 failed, retrying...

• You will have access to 1-2 GB RAM. If you go over 2 GB of RAM the kernel may be restarted.
  • Because we have set up this repo so that you can import pre-processing scripts, you’ll be able to start with any notebook. If your kernel restarts just launch the Binder again!
• If you are inactive for 10 minutes, the session will shut down. Otherwise, you’ll have up to 6 hours of usage or 1 cpu-hour for more intensive runs.
• Any changes that you make will not be saved (please do not attempt to push your work back to this repository). If you would like to save your progress, please refer to #6 in the instructions section.
• Alternatively, if you would like to work on all of this solely locally, you can fork and clone the repository.

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Examples and data used

This binder is modeled after the code tutorials in the HOWTO section of the Giotto website. The goal was to go through the Giotto pipelines with both RNA expression and image (visium) data. This binder should provide a good overview for using Giotto to its fullest potential.

Data

If you want to do some more exploration with the data we used, you can find more information here:

• mini seqFISH
• mini Visium

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Instructions

1. Click this button:
2. Wait for your Docker image to be built (if you want to see how this is done, you can click Build logs to display the running script).
3. Navigate into the Notebooks folder and run whichever notebook you like!
4. Alternatively, navigate into any of the pre-made scripts for a quick look at how some of these steps come together.
5. If you run into any errors or have any questions about how the functions and scripts work, feel free to raise an issue with this repository.
6. If you want to save any of your progress to work on locally, you can download files from the Jupyter notebook directory by clicking the box next to the file name(s) to select it and clicking the Download button on the top left.

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Directory

• Notebooks Directory of notebooks and scripts detailing the tutorials in this binder

  • Scripts Pre-processing scripts for reference and importing in the more advanced tutorial notebooks

    • Creating a Giotto Object

    • Pre-processing steps

    • Clustered Giotto Object

    • Spatial Pre-processed Object

    • Visium Pre-Processed Object

  • Creating a Giotto Object

  • Processing and filtering a Giotto Object

  • Dimensionality Reduction

  • Clustering

  • Differentially Expressed Genes

  • Annnotation Tools

  • Spatial Enrichment

  • Spatial Grid & Network

  • Spatial Gene Detection

  • Spatial Gene Coexpression

  • Hidden Markov Random Field (HMRF) (please note this is a markdown guide to aid in working localy, not a jupyter notebook)

  • Cell-Cell Interaction

  • Interaction Changed Genes

  • Ligand-Receptor Interactions

  • Visium Pre-processing

• Environment file Anaconda environment file with information on the version of R used and the various packages and dependencies necessary for running Giotto