dotools_py.dt.example_10x_processed

dotools_py.dt.example_10x_processed()

Load example scRNAseq from 10x processed.

Loads a reduced version of the example datasets from healthy and malignant B cells from 10x used in the tutorial of the package.

Return type:

AnnData

Returns:

Returns an AnnData object processed with 700 cells and 1851 genes.

Example

>>> import dotools_py as do
>>> adata = do.dt.example_10x_processed()
>>> adata
AnnData object with n_obs × n_vars = 700 × 1851
obs: 'batch', 'condition', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts',
     'total_counts_mt', 'log1p_total_counts_mt', 'pct_counts_mt', 'total_counts_ribo', 'log1p_total_counts_ribo',
     'pct_counts_ribo', 'n_genes', 'n_counts', 'doublet_class', 'doublet_score', 'leiden', 'cell_type', 'autoAnnot',
     'celltypist_conf_score', 'annotation', 'annotation_recluster'
var: 'mean', 'std', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'highly_variable_nbatches',
     'highly_variable_intersection'
uns: 'annotation_colors', 'annotation_recluster_colors', 'batch_colors', 'hvg', 'leiden', 'leiden_colors', 'log1p',
     'neighbors', 'pca', 'umap'
obsm: 'X_CCA', 'X_pca', 'X_umap'
varm: 'PCs'
layers: 'counts', 'logcounts'
obsp: 'connectivities', 'distances'