Data Portal for Single Cell Sequencing

Build an interactive viewer for single-cell RNA sequencing data using public datasets from the CZ CELLxGENE data portal.

Organise project

  1. Create a folder for your project on your computer

  2. Create a data folder outside of your project folder

Get single-cell data

  1. Browse the CELLxGENE collections and find a dataset. For this example we use the Allen Institute Adult Human Brain Atlas - specifically the midbrain (substantia nigra) snRNA-seq dataset.

  2. Download the .h5ad file to your laptop (it is 416.2 MB). The dataset contains 59,505 cells x 58,232 genes with 11 cell types across 3 donors. Key metadata columns include cell_type, cluster_id, supercluster_term, donor_id, and UMAP coordinates in obsm['X_UMAP'].

Get prompting!

  1. In Plan mode, type:
Build an interactive viewer for my single-cell RNA data. The file is at [path/to/data.h5ad].

Result

Single Cell Viewer

Publish to GitHub

Once your app is working, you can save it to GitHub:

Install GitHub CLI

  1. Download GitHub CLI
  2. Authenticate: gh auth login

Upload your code

In chat mode, ask:

Push my project to a new GitHub repository called [your-repo-name]

Or create a repo first:

Create a new private GitHub repository called [your-repo-name], then push my code to it