Data & Setup

Workshop Attendees

If you are attending one of our workshops, you can use Google Colab to run all the code.
If you want to setup your own computer to run the analysis demonstrated on this course, you can follow the instructions below.

Data

The data used in these materials is provided as a zip file. Download and unzip the folder to your Desktop to follow along with the materials.

Software

📦 Installation Instructions (for Google Colab)

How to use in Colab:

  • Open a new notebook in Google Colab

  • Run the commands in code cells.

  • You can now create notebooks and run any of the scripts in Google Colab.

  • If you want to run the notebooks in Colab, you can also use the “Open in Colab” badge below:

Open In Colab

Repository link:
https://cambiotraining.github.io/ml-unsupervised/

2. Run locally

  • Install Python (we recommend using Anaconda or Miniconda to manage your Python environment).

  • Install VSCode (see below) or Spyder.

  • Download the material or clone the repository (optional, for full access)

git clone https://github.com/cambiotraining/ml-unsupervised
  • Install required Python packages
pip install numpy pandas keras tensorflow scikit-learn seaborn matplotlib scanpy pca

or

pip install -r requirements.txt

Visual Studio Code

  • Go to the Visual Studio Code download page and download the installer for your operating system. Double-click the downloaded file to install the software, accepting all the default options.
  • After completing the installation, go to your Windows Menu, search for “Visual Studio Code” and launch the application.
  • Go to “File > Preferences > Settings”, then select “Text Editor > Files” on the drop-down menu on the left. Scroll down to the section named “EOL” and choose “\n” (this will ensure that the files you edit on Windows are compatible with the Linux operating system).
  • Go to the Visual Studio Code download page and download the installer for Mac.
  • Go to the Downloads folder and double-click the file you just downloaded to extract the application. Drag-and-drop the “Visual Studio Code” file to your “Applications” folder.
  • You can now open the installed application to check that it was installed successfully (the first time you launch the application you will get a warning that this is an application downloaded from the internet - you can go ahead and click “Open”).