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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