How to obtain all gene details from each of the clusters formed in UMAP
0
0
Entering edit mode
2.2 years ago
shome ▴ 10

I have sc-RNA seq data which I have processed and analysed to get the following UMAP clusters.Now,I want to extract the gene lists for each of the clusters.But,I am not sure how to do it ? Any suggestions or points on how to proceed ?

enter image description here

Here is how my scanpy object looks like :

> AnnData object with n_obs × n_vars 
>     obs: 'sample', 'n_genes', 'batch', 'n_genes_by_counts', 'total_counts', 'total_counts_mt', 'pct_counts_mt',
> 'total_counts_ribo', 'pct_counts_ribo', 'total_counts_hb',
> 'pct_counts_hb', 'percent_mt2', 'n_counts', 'leiden_1.0',
> 'leiden_0.3', 'leiden_0.2', 'leiden_0.1', 'leiden_0.01'
>     var: 'gene_ids', 'feature_types', 'n_cells-0', 'n_cells-1', 'n_cells-2', 'n_cells-3', 'mt', 'ribo', 'hb', 'n_cells_by_counts',
> 'mean_counts', 'pct_dropout_by_counts', 'total_counts', 'n_cells',
> 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean',
> 'std'
>     uns: 'sample_colors', 'log1p', 'hvg', 'pca', 'neighbors', 'umap', 'leiden', 'leiden_0.3_colors', 'leiden_0.2_colors',
> 'leiden_0.1_colors', 'leiden_1.0_colors', 'dendrogram_sample',
> 'wilcoxon', 'rank_genes_groups'
>     obsm: 'X_pca', 'X_umap'
>     varm: 'PCs'
>     obsp: 'distances', 'connectivities'
scanpy Sc-RNA • 333 views
ADD COMMENT

Login before adding your answer.

Traffic: 1797 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6