kaggle examples

[cornhundred]

Make kaggle examples using public 10X genomics data. The notebooks should be proof of concepts that demonstrate how we can use Clustergrammer2 to perform exploratory data analysis. They should also include static UMAP and t-SNE plots of cells and genes to highlight the relationship of a heatmap and dimensionality reduction views of data points and dimensions.

Make Seurat, Scanpy, and scVI kernels, save their outputs, and visualize them using Clustergrammer2. We can compare the clustering and cell type labels from the different methods in a summary notebook (that loads the saved data from each kernel).

scVI link: https://github.com/YosefLab/scVI/blob/master/tests/notebooks/Linearly_decoded_VAE_for_gene_interpretation.ipynb

[cornhundred]

Kaggle is deprecating their pre-installation of libraries. This requires us to !pip install clustergrammer2 in the notebook, which does not update the front end (requires a page refresh to show widget). Additionally, saving widgets of moderate size fails, which requires an extra step to disable making widgets when committing. Based on this we're suspending development of examples on Kaggle for now.

We will instead focus on MyBinder and Saturn Cloud examples (https://github.com/ismms-himc/clustergrammer2/issues/22)