API Reference

This is a static API inventory for the current source tree. It is intentionally not generated with Sphinx autodoc because the package depends on the Scanpy stack and the docs hub builds in a lightweight documentation environment.

Top-Level Namespace

Source: src/single_cell_python_tools/__init__.py

  • sctl.pp: preprocessing namespace.

  • sctl.pl: plotting namespace.

  • sctl.tl: tools namespace.

  • sctl.DATASET_class: high-level workflow class.

DATASET_class

Source: DATASET_class.py

sctl.pp

Source files:

Public functions:

  • reset_cellxgene_var_names

  • downcast_layers_to_float32

  • annotate_QC_genes

  • calculate_qc_metrics

  • plot_QC_metrics_scatter

  • plot_QC_metrics_violin

  • plot_qc_metrics

  • annotate_n_view_adata_raw_counts

  • basic_filitering

  • filter_cells_by_anotated_QC_gene

  • remove_genes

  • process2scaledPCA

  • scale_func

  • PCA_func

  • norm_log

  • HVG_selection_log_norm_seurat

  • HVG_selection_log_norm_seurat_v3

  • HVG_removal

  • regress_out_anotated_QC_genes

  • calc_cell_cycle_score

  • regress_cell_cycle_score_func

  • leiden_clustering

  • rename_leiden_clusters_old_old

  • rename_leiden_clusters_old

  • rename_leiden_clusters

  • leiden_cluster_sil_score

  • silhouette_walk_Largest_drop

  • silhouette_walk_4_Largest_drops

sctl.pl

Source files:

Public functions:

  • silhouette_score_n_plot

  • silhouette_score_of_obs_key_n_plot

  • plot_batch_obs_key_of_obs_key2

  • plot_adata_row_total_dist

  • plot_adata_raw_and_X_rowdist_old

  • plot_adata_raw_and_X_rowdist

  • plot_batch_obs_key_of_obs_key2_old

  • plot_percent_obs_key2_per_batch_obs_key

sctl.tl

Source: tools/_functions_4_scanpy.py

Public functions:

  • print_size_in_MB

  • df_loadings_ordered_byPC

  • cef_to_adata

  • annotate_marker_genes

  • rank_genes

  • rank_genes_obscat1_vs_obscat2

  • diff_exp

  • GSEA_enrichr_all_clusters

  • filter_obs

  • label_cells_by_single_gene_expression

  • label_cells_by_double_gene_expression

  • average_feature_expression

  • average_obs_feature_per_group

  • make_df_obs_adataX

Direct Module APIs

Source: tools/_ingest_verbose.py

  • ingest_verbose

  • Ingest