chanzuckerberg / cellxgene-documentation Goto Github PK

When a scientist has downloaded or explored data and come to a conclusion based on that effort, they want to know how to cite cellxgene so that they can credit us for the effort.

When a scientist has downloaded or explored data and come to a conclusion based on that effort, they want to know how to cite the data they used so that they can credit the authors when they've benefited from their study.

The Find Data section needs to be replaced to demonstrate the filters for Datasets and Collections.

As in your readme, First, the flask application which is deployed on your server (found in the ‘prep your project’ section of the linked article) should be cellxgene with an appropriate wsgi.py file added as described in the article.
I don't know how to modify this to make it run cellxgene

from myapp import create_app

app = create_app()

if __name__ == "__main__":
    app.run(host='0.0.0.0')

Any help?
Thanks!

Create WMG tutorial

Google Drive Folder

My h5ad anndata object summary:

AnnData object with n_obs × n_vars = 42414 × 25278
    obs: 'group', 'n_genes', 'n_genes_by_counts', 'total_counts', 'total_counts_mt', 'pct_counts_mt', 'leiden', 'merged', 'coarse'
    var: 'gene_ids', 'feature_types', 'mt', 'n_cells_by_counts', 'mean_counts', 'pct_dropout_by_counts', 'total_counts', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm'
    uns: 'log1p', 'hvg', 'pca', 'neighbors', 'umap', 'tsne', 'group_colors', 'leiden', 'leiden_colors', 'rank_genes_groups', 'merged_colors', 'coarse_colors'
    obsm: 'X_pca', 'X_umap', 'X_tsne'
    varm: 'PCs'
    obsp: 'distances', 'connectivities'

On the explorer, there are no 'leiden', 'merged', 'coarse' categories.
For example, the adata.obs['leiden]:

Name: leiden, Length: 42414, dtype: category
Categories (15, object): ['0', '1', '2', '3', ..., '11', '12', '13', '14']

The dtype is the same as adata.obs['group'], I just don't know why leiden category does not show up in the explorer.

I cannot create a new category either, since there's no assignment.

How could I present all obs annotation on the explorer?

Thanks!

Hi,

I have data hosted online, but I am having trouble following the instructions for self-hosting the cellxgene software on Heroku.
Any advice?

Hello!

I am looking to download the anndata file for this cellxgene project:

https://maternal-fetal-interface.cellgeni.sanger.ac.uk/

I don't see it in the data portal, but I see that it is using the cellxgene interface. Is there anyway to download the .h5ad file from this project?

Thank you!

Elze