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Overview
Installation
API
Core
AdataDict Class
anndict.AdataDict.set_hierarchy
anndict.AdataDict.add_stratification
anndict.AdataDict.flatten
anndict.AdataDict.fapply
anndict.AdataDict.fapply_return
anndict.AdataDict.index_bool
anndict.AdataDict.set_obs_index
anndict.AdataDict.set_var_index
anndict.AdataDict.check_structure
anndict.AdataDict.copy
Iterate over AnnDictionaries
anndict.adata_dict.adata_dict_fapply
Build, Write, and Read AnnDictionaries
anndict.adata_dict.build_adata_dict
anndict.adata_dict.add_stratification
anndict.adata_dict.write_adata_dict
anndict.adata_dict.read_adata_dict
anndict.adata_dict.read_adata_dict_from_h5ad
anndict.adata_dict.concatenate_adata_dict
LLM Management
Configure and Call
anndict.configure_llm_backend
anndict.get_llm_config
anndict.call_llm
anndict.retry_call_llm
Annotate
Cells
De Novo
Transfer Labels
Benchmark
Error Correction
Genes
Make Gene Lists
Plot
Module Scores
anndict.plot.module_score_barplot
anndict.plot.module_score_umap
Annotate Genes on Heatmap
anndict.plot.annotate_gene_groups_with_ai_biological_process
Confusion Matrix
anndict.plot.plot_confusion_matrix_from_adata
anndict.plot.plot_confusion_matrix
Sankey Plots
anndict.plot.plot_sankey
anndict.plot.save_sankey
Agreement Bar Plots
anndict.plot.plot_grouped_average
anndict.plot.plot_model_agreement
anndict.plot.plot_model_agreement_categorical
Stabilizing Classifier
anndict.plot.plot_training_history
anndict.plot.plot_label_changes
Automated Label Management
Single Column
anndict.simplify_obs_column
anndict.create_label_hierarchy
anndict.map_cell_type_labels_to_simplified_set
anndict.simplify_var_index
anndict.map_gene_labels_to_simplified_set
Within Adata
anndict.ensure_label_consistency_adata
anndict.ensure_label_consistency_main
Between Adata
anndict.ai_unify_labels
Utils
AnnDictionary
anndict.utils.enforce_semantic_list
anndict.utils.make_names
anndict.utils.normalize_string
anndict.utils.normalize_label
anndict.utils.summarize_metadata
anndict.utils.display_html_summary
anndict.utils.create_color_map
anndict.utils.get_slurm_cores
AnnData
anndict.utils.get_adata_columns
anndict.utils.remove_genes
anndict.utils.add_col_to_adata_obs
anndict.utils.add_col_to_adata_var
anndict.utils.add_col_to_pd_df
anndict.utils.convert_obs_col_to_category
anndict.utils.convert_obs_col_to_string
anndict.utils.convert_obs_index_to_str
anndict.utils.filter_gene_list
Scanpy
anndict.utils.sample_and_drop
anndict.utils.sample_adata_dict
PCA Density Filter
anndict.utils.pca_density_filter_adata
anndict.utils.pca_density_filter_main
Stabilizing Classifier
anndict.utils.stable_label_adata
anndict.utils.stable_label
Read Spatial Data
anndict.utils.build_adata_from_transcript_positions
anndict.utils.build_adata_from_visium
anndict.utils.add_blank_image_to_adata
anndict.utils.read_transcript_coords
anndict.utils.get_steps_and_coords
anndict.utils.populate_sparse_array
anndict.utils.process_gene_counts
anndict.utils.create_anndata
UCE
anndict.utils.uce_adata
Fapply Wrappers
AnnDictionary
anndict.wrappers.remove_genes_adata_dict
anndict.wrappers.ai_annotate_biological_process_adata_dict
anndict.wrappers.simplify_var_index_adata_dict
anndict.wrappers.ensure_label_consistency_adata_dict
anndict.wrappers.simplify_obs_column_adata_dict
anndict.wrappers.create_label_hierarchy_adata_dict
anndict.wrappers.ai_annotate_cell_type_adata_dict
anndict.wrappers.ai_compare_cell_type_labels_pairwise_adata_dict
anndict.wrappers.ai_annotate_cell_sub_type_adata_dict
anndict.wrappers.ai_determine_leiden_resolution_adata_dict
anndict.wrappers.harmony_label_transfer_adata_dict
anndict.wrappers.plot_sankey_adata_dict
anndict.wrappers.save_sankey_adata_dict
anndict.wrappers.plot_grouped_average_adata_dict
anndict.wrappers.plot_label_changes_adata_dict
anndict.wrappers.plot_confusion_matrix_adata_dict
anndict.wrappers.summarize_metadata_adata_dict
anndict.wrappers.display_html_summary_adata_dict
anndict.wrappers.pca_density_adata_dict
Scanpy
anndict.wrappers.sample_and_drop_adata_dict
anndict.wrappers.normalize_adata_dict
anndict.wrappers.log_transform_adata_dict
anndict.wrappers.set_high_variance_genes_adata_dict
anndict.wrappers.rank_genes_groups_adata_dict
anndict.wrappers.scale_adata_dict
anndict.wrappers.pca_adata_dict
anndict.wrappers.neighbors_adata_dict
anndict.wrappers.leiden_adata_dict
anndict.wrappers.leiden_sub_cluster
anndict.wrappers.leiden_sub_cluster_adata_dict
anndict.wrappers.calculate_umap_adata_dict
anndict.wrappers.plot_umap_adata_dict
Squidpy
Tutorials
Using the AdataDict Class
Build an AdataDict
Manipulate the Hierarchy of an AdataDict
Iterate Over an AdataDict
Write and Read AdataDict
Annotating with AnnDictionary
Automated Cell Type Marker Gene Scores
Cell Type Annotation with Large Language Models (LLMs)
Transfer Labels Using an Sklearn Classifier
Automated Annotation of Spatial Transcriptomics
Contribute
.rst
.pdf
Error Correction
Error Correction
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