pp.prepare_data_for_phemd(adata, sample_col)
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Convert the expression data to the input format of PhEMD (R implementation) |
pp.convert_cell_types_to_phemd_format(adata, ...)
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Converts adata to the tables required by PhEMD (R implementation) and saves them to output_dir |
pp.calculate_compositional_metrics(adata, ...)
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Calculate compositional metrics for the given AnnData object. |
pp.calculate_cell_qc_metrics(adata, ...[, ...])
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Calculate agregated cell quality control metrics for the given AnnData object |
pp.calculate_n_cells_per_sample(adata, ...)
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Calculate the number of cells per sample in the given AnnData object. |
pp.filter_small_samples(adata, sample_key[, ...])
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Leave only samples with not less than sample_size_threshold cells |
pp.filter_small_cell_groups(adata, ...[, ...])
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Leave only cell groups with not less than cluster_size_threshold cells |
pp.subsample(adata, obs_category_col, ...[, ...])
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Subsample cells from each category in obs_category_col to have at least min_samples_per_category cells. |
pp.is_count_data(matrix[, window_size])
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Ensure that matrix only contains integers |
pp.fill_nan_distances(distances[, ...])
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Fill NaN values in distances with maximum distance multiplied by n_max_distances |
