CELLxGENE is an an interactive explorer for single-cell transcriptomics data. It can be very useful to explore your recently analyzed single-cell dataset or a dataset you just downloaded from a repository
- You have already intalled Ubuntu through WSL on your windows machine, along with conda. Or you have a machine with any Linux distribution and conda isntalled
The first line creates a conda environment called cellxgene and installs python in it. The second activates it
conda create --name cellxgene python
conda activate cellxgene
Now you can use pip to install cellxgene:
pip install cellxgene
cellxgene can open files with h5ad extension. Locate your file and open it with something like:
cellxgene launch /mnt/c/Users/my_username/Downloads/aorta.h5ad
Click on the resulting URL and a new tab will open in your browser. Do not close the terminal!
After you are done, you can press ctrl+c to exit cellxgene process or just close the terminal.
If you want to know more about how to access the files saved on your machine from within your Ubuntu isntalation, you can read more here