How to obtain all gene details from each of the clusters formed in UMAP
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2.7 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 ?

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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 • 388 views
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