Index

_

__attributes__ (larry._datasets._url_path_interfaces.URLPathInterface property) __author__ (in module larry._analysis) (in module larry._analysis._calculate_dominate_fate) (in module larry._analysis._count_clones_by_timepoint) (in module larry._analysis._estimate_growth_rates) (in module larry._analysis._get_annotated_metadata_d2_lineage_cells) (in module larry._analysis._get_lineage_obs) (in module larry._analysis._growth_rate_grouped_violin_plot) (in module larry._callbacks._interpolation_task) __build__() (larry._utils._abc_parse.ABCParse method) (larry._utils.ABCParse method) __call__() (larry._analysis._LARRY_t0_test_indices.LARRY_t0_test_indices method) (larry._analysis.LARRY_t0_test_indices method) (larry._datasets._anndata_configuration.ExpressionMatrix method) (larry._datasets._data.DataHandler method) (larry._datasets._directory_manager.DirectoryManager method) (larry._datasets._split_data.SplitDataForTask method) (larry._datasets.klein_lab_pp_recipe._running_quantile.RunningQuantile method) (larry._datasets.klein_lab_pp_recipe.RunningQuantile method) (larry._datasets.RunningQuantile method) (larry._datasets.SplitDataForTask method) (larry._tools._cell_fates.CellFates method) (larry._tools._count_fate_values.FateValues method) (larry._tools.CellFates method) (larry._utils._accuracy_scores.AccuracyScores method) (larry._utils._auto_parse_base_class.AutoParseBase method) (larry._utils._confusion_matrix.ConfusionMatrix method) (larry._utils._count_fate_values.FateValues method) (larry._utils._model_evaluator.ModelEvaluator method) (larry._utils._multi_fated_lineage_prediction_results.MultifatedLineagePredictionResults method) (larry._utils._multiclass_precision_recall.MulticlassPrecisionRecall method) (larry._utils.AutoParseBase method) (larry._utils.MultifatedLineagePredictionResults method) __collect__() (larry._utils._auto_parse_base_class.AutoParseBase method) (larry._utils.AutoParseBase method) __configure__() (larry._datasets._dimension_reduction.DimensionReduction method) (larry._datasets.DimensionReduction method) __doc__ (in module larry._callbacks._interpolation_task) __email__ (in module larry._analysis) (in module larry._analysis._calculate_dominate_fate) (in module larry._analysis._count_clones_by_timepoint) (in module larry._analysis._estimate_growth_rates) (in module larry._analysis._get_annotated_metadata_d2_lineage_cells) (in module larry._analysis._get_lineage_obs) (in module larry._analysis._growth_rate_grouped_violin_plot) (in module larry._callbacks._interpolation_task) __heatmap__() (larry._utils._confusion_matrix.ConfusionMatrix method) __hide__() (larry._utils._auto_parse_base_class.AutoParseBase method) (larry._utils.AutoParseBase method) __init_kwargs__() (larry._utils._auto_parse_base_class.AutoParseBase method) (larry._utils.AutoParseBase method) __mkdir__() (larry._datasets._directory_manager.DirectoryManager method) __module_name__ (in module larry._analysis) (in module larry._analysis._calculate_dominate_fate) (in module larry._analysis._count_clones_by_timepoint) (in module larry._analysis._estimate_growth_rates) (in module larry._analysis._get_annotated_metadata_d2_lineage_cells) (in module larry._analysis._get_lineage_obs) (in module larry._analysis._growth_rate_grouped_violin_plot) (in module larry._callbacks._interpolation_task) __parse__() (larry._tools._cell_fates.CellFates method) (larry._tools.CellFates method) (larry._utils._abc_parse.ABCParse method) (larry._utils._auto_parse_base_class.AutoParseBase method) (larry._utils.ABCParse method) (larry._utils.AutoParseBase method) __repr__() (larry._datasets._anndata_path_manager.AnnDataPathManager method) (larry._datasets._url_path_interfaces.URLPathInterface method) (larry._datasets.AnnDataPathManager method) (larry._utils._model_evaluator.ModelEvaluator method) __set__() (larry._utils._abc_parse.ABCParse method) (larry._utils.ABCParse method) __set_existing__() (larry._utils._abc_parse.ABCParse method) (larry._utils.ABCParse method) __setup__() (larry._tools._cell_fates.CellFates method) (larry._tools.CellFates method) __update__() (larry._utils._abc_parse.ABCParse method) (larry._utils.ABCParse method) _ANNOT (larry._utils._confusion_matrix.ConfusionMatrix property) _annotate_cell_count() (in module larry._analysis._growth_rate_grouped_violin_plot) _annotate_celltype() (in module larry._analysis._growth_rate_grouped_violin_plot) _attrs (larry._datasets._url_path_interfaces.URLPathInterface property) _background_scatter_UMAP() (in module larry._analysis._estimate_growth_rates) _BUILT (larry._utils._abc_parse.ABCParse attribute) (larry._utils.ABCParse attribute) _calculate_growth_rate_from_counts() (in module larry._analysis._estimate_growth_rates) _call_params (larry._utils._auto_parse_base_class.AutoParseBase property) (larry._utils.AutoParseBase property) _collect_literal_kwargs() (larry._utils._auto_parse_base_class.AutoParseBase method) (larry._utils.AutoParseBase method) _collected_params (larry._utils._auto_parse_base_class.AutoParseBase property) (larry._utils.AutoParseBase property)

_compose_major_fate_df() (in module larry._analysis._calculate_dominate_fate) _compose_target_pred_df() (larry._utils._multi_fated_lineage_prediction_results.MultifatedLineagePredictionResults method) (larry._utils.MultifatedLineagePredictionResults method) _compute_error() (larry._utils._multi_fated_lineage_prediction_results.MultifatedLineagePredictionResults method) (larry._utils.MultifatedLineagePredictionResults method) _configure_fates() (larry._tools._cell_fates.CellFates method) (larry._tools.CellFates method) _configure_lineage_traced_time_subset() (larry._tools._index_subsets.IndexSubsets method) (larry._tools.IndexSubsets method) (larry._utils._count_fate_values.IndexSubsets method) _configure_time_subset() (larry._tools._index_subsets.IndexSubsets method) (larry._tools.IndexSubsets method) (larry._utils._count_fate_values.IndexSubsets method) _count_d2_daughter_cells() (in module larry._analysis._count_d2_daughter_cells) _count_daughter_cells() (in module larry._analysis._count_d2_daughter_cells) _count_values_at_lineage_fate() (larry._tools._count_fate_values.FateValues method) (larry._utils._count_fate_values.FateValues method) _d2_lineage_cell_idx() (in module larry._analysis._estimate_growth_rates) _dataset (larry._datasets._data.CytokinePerturbationData attribute) (larry._datasets._data.inVitroData attribute) (larry._datasets._data.inVivoData attribute) (larry._datasets._in_vitro_dataset.inVitroDataset attribute) (larry._datasets._url_path_interfaces.CytokinePerturbationURLPaths attribute) (larry._datasets._url_path_interfaces.inVitroURLPaths attribute) (larry._datasets._url_path_interfaces.inVivoURLPaths attribute) (larry._datasets.CytokinePerturbationData attribute) (larry._datasets.CytokinePerturbationURLPaths attribute) (larry._datasets.inVitroData attribute) (larry._datasets.inVitroURLPaths attribute) (larry._datasets.inVivoData attribute) (larry._datasets.inVivoURLPaths attribute) _description (larry._datasets._url_path_interfaces.URLPathInterface property) _download_path (larry._datasets._url_path_interfaces.FormattedURLFile property) _download_structure (larry._datasets._url_path_interfaces.CytokinePerturbationURLPaths attribute) (larry._datasets._url_path_interfaces.inVitroURLPaths attribute) (larry._datasets._url_path_interfaces.inVivoURLPaths attribute) (larry._datasets.CytokinePerturbationURLPaths attribute) (larry._datasets.inVitroURLPaths attribute) (larry._datasets.inVivoURLPaths attribute) _enumerate_time_pairs() (in module larry._analysis._estimate_growth_rates) _f_hat_fates (larry._utils._multiclass_precision_recall.MulticlassPrecisionRecall property) _f_obs_fates (larry._utils._multiclass_precision_recall.MulticlassPrecisionRecall property) _fate_bias_matrix() (larry._utils._model_evaluator.ModelEvaluator method) _fates_missing_from_f_hat (larry._utils._multiclass_precision_recall.MulticlassPrecisionRecall property) _fates_missing_from_f_obs (larry._utils._multiclass_precision_recall.MulticlassPrecisionRecall property) _fname (larry._datasets._url_path_interfaces.FormattedURLFile property) _format() (larry._datasets._url_path_interfaces.URLPathInterface method) _format_ticks() (larry._analysis._growth_rate_grouped_violin_plot.ViolinPlot method) _get_plot_vmin_vmax() (in module larry._analysis._estimate_growth_rates) _has_t() (in module larry._tools._time_occupance) (in module larry._utils._count_fate_values) _header (larry._datasets._url_path_interfaces.URLPathInterface property) _init_params (larry._utils._auto_parse_base_class.AutoParseBase property) (larry._utils.AutoParseBase property) _inspect() (larry._utils._auto_parse_base_class.AutoParseBase method) (larry._utils.AutoParseBase method) _is_d2() (in module larry._analysis._count_d2_daughter_cells) _is_d2_clone() (in module larry._analysis._count_d2_daughter_cells) _is_np_array() (in module larry._analysis._count_d2_daughter_cells) _lineage_state_descriptions() (larry._tools._cell_fates.CellFates method) (larry._tools.CellFates method) _mk_plot() (larry._analysis._growth_rate_grouped_violin_plot.ViolinPlot method) _MODEL_TYPE (larry._utils._model_evaluator.ModelEvaluator property) _parse_params (larry._utils._auto_parse_base_class.AutoParseBase property) (larry._utils.AutoParseBase property) _path_constructor() (larry._datasets._anndata_path_manager.AnnDataPathManager method) (larry._datasets.AnnDataPathManager method) _plot_continuous_highlight_UMAP() (in module larry._analysis._estimate_growth_rates) _plot_fate_bias_clustermap() (larry._utils._task_two_eval_callback.TaskTwoEvalCallback method) (larry._utils.TaskTwoEvalCallback method) _predict_state() (larry._utils._model_evaluator.ModelEvaluator method) _predicted_label() (larry._utils._multi_fated_lineage_prediction_results.MultifatedLineagePredictionResults method) (larry._utils.MultifatedLineagePredictionResults method) _read_format_df() (in module larry._datasets._anndata_configuration) _set_violinplot_line_colors() (in module larry._analysis._growth_rate_grouped_violin_plot) _STORED (larry._utils._abc_parse.ABCParse property) (larry._utils.ABCParse property) _sum_normalize_fate() (in module larry._tools._cell_fates) _target_label() (larry._utils._multi_fated_lineage_prediction_results.MultifatedLineagePredictionResults method) (larry._utils.MultifatedLineagePredictionResults method) _TESTING (larry._utils._task_two_eval_callback.TaskTwoEvalCallback property) (larry._utils.TaskTwoEvalCallback property) _to_frame() (larry._utils._accuracy_scores.AccuracyScores method) _url_paths (larry._datasets._data.CytokinePerturbationData attribute) (larry._datasets._data.inVitroData attribute) (larry._datasets._data.inVivoData attribute) (larry._datasets._in_vitro_dataset.inVitroDataset attribute) (larry._datasets.CytokinePerturbationData attribute) (larry._datasets.inVitroData attribute) (larry._datasets.inVivoData attribute) _VMAX (larry._utils._confusion_matrix.ConfusionMatrix property)

A

ABCParse (class in larry._utils) (class in larry._utils._abc_parse) AccuracyScores (class in larry._utils._accuracy_scores) adata (larry._datasets._anndata_configuration.AnnDataConfiguration property) (larry._datasets.AnnDataConfiguration property) AnnDataConfiguration (class in larry._datasets) (class in larry._datasets._anndata_configuration) AnnDataPathManager (class in larry._datasets) (class in larry._datasets._anndata_path_manager)

annotate_clone_idx_in_obs() (in module larry._tools) (in module larry._tools._annotate_clone_idx_in_obs) annotate_fated() (in module larry._tools) (in module larry._tools._annotate_fated) (in module larry._utils._count_fate_values) AutoParseBase (class in larry._utils) (class in larry._utils._auto_parse_base_class)

C

calculate_dominate_fate() (in module larry._analysis) (in module larry._analysis._calculate_dominate_fate) cell_cycle_genes() (in module larry._datasets) (in module larry._datasets.klein_lab_pp_recipe) (in module larry._datasets.klein_lab_pp_recipe._cell_cycle_genes) CellFates (class in larry._tools) (class in larry._tools._cell_fates) clone_matrix (larry._datasets._url_path_interfaces.URLPathInterface property) clustermap() (larry._tools._cell_fates.CellFates method) (larry._tools.CellFates method) combine_fate_matrices() (larry._tools._cell_fates.CellFates method) (larry._tools.CellFates method) compose_adata() (larry._datasets._data.DataHandler method) concat_train_test() (larry._datasets._split_data.SplitDataForTask method) (larry._datasets.SplitDataForTask method) conf_mtx (larry._utils._confusion_matrix.ConfusionMatrix property) configure_eval_data() (larry._callbacks._interpolation_task.InterpolationTask method) (larry._callbacks.InterpolationTask method)

ConfusionMatrix (class in larry._utils._confusion_matrix) count_clonal_lineages() (in module larry._analysis) (in module larry._analysis._count_clonal_lineages) count_clones_by_timepoint() (in module larry._analysis) (in module larry._analysis._count_clones_by_timepoint) count_d2_daughter_cells() (in module larry._analysis) (in module larry._analysis._count_d2_daughter_cells) count_fate_values() (in module larry._tools) (in module larry._tools._count_fate_values) (in module larry._utils._count_fate_values) count_t0_cell_fates() (in module larry._tools._count_fate_values) (in module larry._utils._count_fate_values) CytokinePerturbationData (class in larry._datasets) (class in larry._datasets._data) CytokinePerturbationURLPaths (class in larry._datasets) (class in larry._datasets._url_path_interfaces)

D

d2_cell_fate_matrix() (in module larry._tools._count_fate_values) (in module larry._utils._count_fate_values) DataHandler (class in larry._datasets._data) DaughterCellPlots (class in larry._analysis._count_d2_daughter_cells)

DimensionReduction (class in larry._datasets) (class in larry._datasets._dimension_reduction) DirectoryManager (class in larry._datasets._directory_manager) download() (larry._datasets._url_path_interfaces.URLPathInterface method) downloaded (larry._datasets._url_path_interfaces.FormattedURLFile property)

E

estimate_growth_rates() (in module larry._analysis) (in module larry._analysis._estimate_growth_rates)

ExpressionMatrix (class in larry._datasets._anndata_configuration) (class in larry._datasets._load_expr_matrix)

F

F_hat (larry._utils._task_two_eval_callback.TaskTwoEvalCallback property) (larry._utils.TaskTwoEvalCallback property) F_obs (larry._utils._multiclass_precision_recall.MulticlassPrecisionRecall property) (larry._utils._task_two_eval_callback.TaskTwoEvalCallback property) (larry._utils.TaskTwoEvalCallback property) F_obs_impure (larry._utils._lineage_classification.LineageClassification property) (larry._utils.LineageClassification property) F_obs_pred (larry._utils._task_two_eval_callback.TaskTwoEvalCallback property) (larry._utils.TaskTwoEvalCallback property) F_obs_pure (larry._utils._lineage_classification.LineageClassification property) (larry._utils.LineageClassification property) fate_df (larry._utils._task_two_eval_callback.TaskTwoEvalCallback property) (larry._utils.TaskTwoEvalCallback property) fate_prediction (larry._datasets._anndata_path_manager.AnnDataPathManager property) (larry._datasets.AnnDataPathManager property) fate_prediction() (larry._datasets._data.inVitroData method) (larry._datasets._in_vitro_dataset.inVitroDataset method) (larry._datasets.inVitroData method) fate_prediction_h5ad_path (larry._datasets._data.DataHandler property) fate_prediction_subsetes (larry._utils._accuracy_scores.AccuracyScores property) fated_idx() (in module larry._tools._annotate_fated) (in module larry._utils._count_fate_values)

fates (larry._tools._cell_fates.CellFates property) (larry._tools.CellFates property) (larry._utils._multiclass_precision_recall.MulticlassPrecisionRecall property) FateValues (class in larry._tools._count_fate_values) (class in larry._utils._count_fate_values) fetch_data() (in module larry._utils) (in module larry._utils._fetch_data) fetch_fate_bias_data() (in module larry._tools) (in module larry._tools._fetch_fate_bias_data) filter_fate() (in module larry._tools._time_occupance) (in module larry._utils._count_fate_values) format_state_for_merge() (larry._tools._cell_fates.CellFates method) (larry._tools.CellFates method) FormattedURLFile (class in larry._datasets._url_path_interfaces) forward() (larry._utils._accuracy_scores.AccuracyScores method) (larry._utils._multiclass_precision_recall.MulticlassPrecisionRecall method) forward_with_grad() (larry._callbacks._interpolation_task.InterpolationTask method) (larry._callbacks.InterpolationTask method) forward_without_grad() (larry._callbacks._interpolation_task.InterpolationTask method) (larry._callbacks.InterpolationTask method) fpath (larry._datasets._url_path_interfaces.FormattedURLFile property) future_time (larry._analysis._LARRY_t0_test_indices.LARRY_t0_test_indices property) (larry._analysis.LARRY_t0_test_indices property)

G

gene_filtered (larry._datasets._anndata_path_manager.AnnDataPathManager property) (larry._datasets.AnnDataPathManager property) gene_filtered_h5ad_path (larry._datasets._data.DataHandler property) gene_names (larry._datasets._url_path_interfaces.URLPathInterface property) get_annotated_metadata_d2_lineage_cells() (in module larry._analysis) (in module larry._analysis._get_annotated_metadata_d2_lineage_cells)

get_lineage_obs() (in module larry._analysis) (in module larry._analysis._get_lineage_obs) growth_rate_grouped_violin_plot() (in module larry._analysis) (in module larry._analysis._growth_rate_grouped_violin_plot)

H

highly_variable_genes() (in module larry._datasets) (in module larry._datasets.klein_lab_pp_recipe) (in module larry._datasets.klein_lab_pp_recipe._highly_variable_genes)

homogeneity (larry._utils._lineage_classification.LineageClassification property) (larry._utils.LineageClassification property)

I

impure_idx_mask (larry._utils._lineage_classification.LineageClassification property) (larry._utils.LineageClassification property) IndexSubsets (class in larry._tools) (class in larry._tools._index_subsets) (class in larry._utils._count_fate_values) info (in module larry._datasets._data) InterpolationTask (class in larry._callbacks) (class in larry._callbacks._interpolation_task)

inVitroData (class in larry._datasets) (class in larry._datasets._data) inVitroDataset (class in larry._datasets._in_vitro_dataset) inVitroURLPaths (class in larry._datasets) (class in larry._datasets._url_path_interfaces) inVivoData (class in larry._datasets) (class in larry._datasets._data) inVivoURLPaths (class in larry._datasets) (class in larry._datasets._url_path_interfaces)

L

labels (larry._utils._confusion_matrix.ConfusionMatrix property) (larry._utils._task_two_eval_callback.TaskTwoEvalCallback property) (larry._utils.TaskTwoEvalCallback property) larry module larry._analysis module larry._analysis._calculate_dominate_fate module larry._analysis._count_clonal_lineages module larry._analysis._count_clones_by_timepoint module larry._analysis._count_d2_daughter_cells module larry._analysis._estimate_growth_rates module larry._analysis._get_annotated_metadata_d2_lineage_cells module larry._analysis._get_lineage_obs module larry._analysis._growth_rate_grouped_violin_plot module larry._analysis._LARRY_t0_test_indices module larry._analysis._temporal_cmap module larry._callbacks module larry._callbacks._interpolation_task module larry._datasets module larry._datasets._anndata_configuration module larry._datasets._anndata_path_manager module larry._datasets._data module larry._datasets._dataset_utils module larry._datasets._dataset_utils._messages module larry._datasets._dimension_reduction module larry._datasets._directory_manager module larry._datasets._in_vitro_dataset module larry._datasets._load_expr_matrix module larry._datasets._split_data module larry._datasets._url_path_interfaces module larry._datasets.klein_lab_pp_recipe module larry._datasets.klein_lab_pp_recipe._cell_cycle_genes module larry._datasets.klein_lab_pp_recipe._highly_variable_genes module larry._datasets.klein_lab_pp_recipe._remove_cell_cycle_correlated_genes module larry._datasets.klein_lab_pp_recipe._running_quantile module larry._datasets.klein_lab_pp_recipe._vscores module

larry._tools module larry._tools._annotate_clone_idx_in_obs module larry._tools._annotate_fated module larry._tools._cell_fates module larry._tools._count_fate_values module larry._tools._fetch_fate_bias_data module larry._tools._index_subsets module larry._tools._subset_clonal module larry._tools._time_occupance module larry._tools._to_anndataset module larry._utils module larry._utils._abc_parse module larry._utils._accuracy_scores module larry._utils._auto_parse_base_class module larry._utils._confusion_matrix module larry._utils._count_fate_values module larry._utils._fetch_data module larry._utils._larry_in_vitro_cmap module larry._utils._lineage_classification module larry._utils._model_evaluator module larry._utils._multi_fate_color_map module larry._utils._multi_fated_lineage_prediction_results module larry._utils._multiclass_precision_recall module larry._utils._sparse_mtx_operations module larry._utils._task_two_eval_callback module LARRY_in_vitro_cmap (in module larry._utils) (in module larry._utils._larry_in_vitro_cmap) LARRY_t0_test_indices (class in larry._analysis) (class in larry._analysis._LARRY_t0_test_indices) lineage_state_descriptions (larry._tools._cell_fates.CellFates property) (larry._tools.CellFates property) lineage_traced (larry._tools._index_subsets.IndexSubsets property) (larry._tools.IndexSubsets property) (larry._utils._count_fate_values.IndexSubsets property) LineageClassification (class in larry._utils) (class in larry._utils._lineage_classification) load_expr_matrix() (in module larry._datasets) (in module larry._datasets._load_expr_matrix) LOGPATH (larry._utils._task_two_eval_callback.TaskTwoEvalCallback property) (larry._utils.TaskTwoEvalCallback property)

M

mean_center() (in module larry._utils) (in module larry._utils._sparse_mtx_operations) Messages (class in larry._datasets._dataset_utils) (class in larry._datasets._dataset_utils._messages) metadata (larry._datasets._url_path_interfaces.URLPathInterface property) mk_multifate_cmap() (in module larry._utils) (in module larry._utils._multi_fate_color_map) mk_plot() (larry._analysis._count_d2_daughter_cells.DaughterCellPlots method) mkdir() (in module larry._datasets) (in module larry._datasets._directory_manager) ModelEvaluator (class in larry._utils._model_evaluator) module larry larry._analysis larry._analysis._calculate_dominate_fate larry._analysis._count_clonal_lineages larry._analysis._count_clones_by_timepoint larry._analysis._count_d2_daughter_cells larry._analysis._estimate_growth_rates larry._analysis._get_annotated_metadata_d2_lineage_cells larry._analysis._get_lineage_obs larry._analysis._growth_rate_grouped_violin_plot larry._analysis._LARRY_t0_test_indices larry._analysis._temporal_cmap larry._callbacks larry._callbacks._interpolation_task larry._datasets larry._datasets._anndata_configuration larry._datasets._anndata_path_manager larry._datasets._data larry._datasets._dataset_utils larry._datasets._dataset_utils._messages larry._datasets._dimension_reduction larry._datasets._directory_manager larry._datasets._in_vitro_dataset larry._datasets._load_expr_matrix larry._datasets._split_data larry._datasets._url_path_interfaces larry._datasets.klein_lab_pp_recipe larry._datasets.klein_lab_pp_recipe._cell_cycle_genes larry._datasets.klein_lab_pp_recipe._highly_variable_genes larry._datasets.klein_lab_pp_recipe._remove_cell_cycle_correlated_genes larry._datasets.klein_lab_pp_recipe._running_quantile larry._datasets.klein_lab_pp_recipe._vscores larry._tools larry._tools._annotate_clone_idx_in_obs larry._tools._annotate_fated larry._tools._cell_fates larry._tools._count_fate_values larry._tools._fetch_fate_bias_data larry._tools._index_subsets larry._tools._subset_clonal larry._tools._time_occupance larry._tools._to_anndataset larry._utils larry._utils._abc_parse larry._utils._accuracy_scores larry._utils._auto_parse_base_class larry._utils._confusion_matrix larry._utils._count_fate_values larry._utils._fetch_data larry._utils._larry_in_vitro_cmap larry._utils._lineage_classification larry._utils._model_evaluator larry._utils._multi_fate_color_map larry._utils._multi_fated_lineage_prediction_results larry._utils._multiclass_precision_recall larry._utils._sparse_mtx_operations larry._utils._task_two_eval_callback

mtx_to_npz() (larry._datasets._dataset_utils._messages.Messages method) (larry._datasets._dataset_utils.Messages method) MulticlassPrecisionRecall (class in larry._utils._multiclass_precision_recall) MultiFateColorMap (in module larry._utils._multi_fate_color_map) MultifatedLineagePredictionResults (class in larry._utils) (class in larry._utils._multi_fated_lineage_prediction_results)

N

n_impure (larry._utils._lineage_classification.LineageClassification property) (larry._utils.LineageClassification property) n_pure (larry._utils._lineage_classification.LineageClassification property) (larry._utils.LineageClassification property) NoneType (in module larry._analysis._temporal_cmap) (in module larry._tools._time_occupance) (in module larry._tools._to_anndataset) (in module larry._utils._abc_parse) (in module larry._utils._accuracy_scores) (in module larry._utils._confusion_matrix) (in module larry._utils._count_fate_values) (in module larry._utils._multiclass_precision_recall)

normalize_variance() (in module larry._utils) (in module larry._utils._sparse_mtx_operations) normed_counts (larry._datasets._url_path_interfaces.URLPathInterface property) note (in module larry._datasets._data) (larry._datasets._dataset_utils._messages.Messages property) (larry._datasets._dataset_utils.Messages property) notify() (larry._datasets._directory_manager.DirectoryManager method) npz_exists (larry._datasets._anndata_configuration.ExpressionMatrix property) (larry._datasets._load_expr_matrix.ExpressionMatrix property) npz_path (larry._datasets._anndata_configuration.ExpressionMatrix property) (larry._datasets._load_expr_matrix.ExpressionMatrix property)

O

obs (larry._datasets._anndata_configuration.AnnDataConfiguration property) (larry._datasets._data.DataHandler property) (larry._datasets.AnnDataConfiguration property)

on_fit_end() (larry._utils._task_two_eval_callback.TaskTwoEvalCallback method) (larry._utils.TaskTwoEvalCallback method) on_train_epoch_end() (larry._callbacks._interpolation_task.InterpolationTask method) (larry._callbacks.InterpolationTask method)

P

PCA (larry._datasets._dimension_reduction.DimensionReduction property) (larry._datasets.DimensionReduction property) plot_growth_rate_UMAPs() (in module larry._analysis._estimate_growth_rates) plot_growth_rates() (in module larry._analysis) (in module larry._analysis._estimate_growth_rates)

plot_hist() (larry._analysis._count_d2_daughter_cells.DaughterCellPlots method) plot_umap() (larry._analysis._count_d2_daughter_cells.DaughterCellPlots method) prepare_data_for_violin_plot() (in module larry._analysis._growth_rate_grouped_violin_plot) pure_idx_mask (larry._utils._lineage_classification.LineageClassification property) (larry._utils.LineageClassification property)

R

raw (larry._datasets._anndata_path_manager.AnnDataPathManager property) (larry._datasets.AnnDataPathManager property) raw_h5ad_path (larry._datasets._data.DataHandler property) read_h5ad() (larry._datasets._data.DataHandler method) read_mtx() (larry._datasets._anndata_configuration.ExpressionMatrix method) (larry._datasets._load_expr_matrix.ExpressionMatrix method) reading_fate_prediction_preprocessed_h5ad() (larry._datasets._dataset_utils._messages.Messages method) (larry._datasets._dataset_utils.Messages method) reading_gene_filtered_h5ad() (larry._datasets._dataset_utils._messages.Messages method) (larry._datasets._dataset_utils.Messages method) reading_raw_h5ad() (larry._datasets._dataset_utils._messages.Messages method) (larry._datasets._dataset_utils.Messages method)

reading_timepoint_recovery_preprocessed_h5ad() (larry._datasets._dataset_utils._messages.Messages method) (larry._datasets._dataset_utils.Messages method) reading_uniformly_preprocessed_h5ad() (larry._datasets._dataset_utils._messages.Messages method) (larry._datasets._dataset_utils.Messages method) remove_cell_cycle_correlated_genes() (in module larry._datasets) (in module larry._datasets.klein_lab_pp_recipe) (in module larry._datasets.klein_lab_pp_recipe._remove_cell_cycle_correlated_genes) RunningQuantile (class in larry._datasets) (class in larry._datasets.klein_lab_pp_recipe) (class in larry._datasets.klein_lab_pp_recipe._running_quantile)

S

save_mtx_as_npz() (larry._datasets._anndata_configuration.ExpressionMatrix method) (larry._datasets._load_expr_matrix.ExpressionMatrix method) Scaler (larry._datasets._dimension_reduction.DimensionReduction property) (larry._datasets.DimensionReduction property) sparse_rowwise_multiply() (in module larry._utils) (in module larry._utils._sparse_mtx_operations) sparse_var() (in module larry._utils) (in module larry._utils._sparse_mtx_operations) sparse_zscore() (in module larry._utils) (in module larry._utils._sparse_mtx_operations) split_for_fate_prediction_task() (in module larry._datasets) (in module larry._datasets._split_data) split_for_timepoint_recovery_task() (in module larry._datasets) (in module larry._datasets._split_data)

split_for_transfer_learning_task() (in module larry._datasets) (in module larry._datasets._split_data) split_path (larry._datasets._directory_manager.DirectoryManager property) SplitDataForTask (class in larry._datasets) (class in larry._datasets._split_data) state_description_at_time() (in module larry._tools._cell_fates) state_to_cell_indexed_fate_bias() (larry._tools._cell_fates.CellFates method) (larry._tools.CellFates method) subset() (larry._tools._cell_fates.CellFates method) (larry._tools.CellFates method) subset_clonal() (in module larry._tools) (in module larry._tools._subset_clonal)

T

t (larry._utils._model_evaluator.ModelEvaluator property) (larry._utils._task_two_eval_callback.TaskTwoEvalCallback property) (larry._utils.TaskTwoEvalCallback property) t0_idx (larry._utils._task_two_eval_callback.TaskTwoEvalCallback property) (larry._utils.TaskTwoEvalCallback property) t0_obs (larry._analysis._LARRY_t0_test_indices.LARRY_t0_test_indices property) (larry._analysis.LARRY_t0_test_indices property) t_elapsed_message() (larry._datasets._split_data.SplitDataForTask method) (larry._datasets.SplitDataForTask method) TaskTwoEvalCallback (class in larry._utils) (class in larry._utils._task_two_eval_callback) temporal_cmap() (in module larry._analysis) (in module larry._analysis._temporal_cmap) temporal_fate_descriptions() (larry._tools._cell_fates.CellFates method) (larry._tools.CellFates method) test_idx (larry._datasets._split_data.SplitDataForTask property) (larry._datasets.SplitDataForTask property) test_lineages (larry._analysis._LARRY_t0_test_indices.LARRY_t0_test_indices property) (larry._analysis.LARRY_t0_test_indices property)

time_occupance() (in module larry._tools) (in module larry._tools._time_occupance) (in module larry._utils._count_fate_values) timepoint_recovery (larry._datasets._anndata_path_manager.AnnDataPathManager property) (larry._datasets.AnnDataPathManager property) timepoint_recovery() (larry._datasets._data.inVitroData method) (larry._datasets._in_vitro_dataset.inVitroDataset method) (larry._datasets.inVitroData method) timepoint_recovery_h5ad_path (larry._datasets._data.DataHandler property) to_AnnDataset() (in module larry._tools) (in module larry._tools._to_anndataset) to_h5ad() (larry._datasets._data.DataHandler method) train_idx (larry._datasets._split_data.SplitDataForTask property) (larry._datasets.SplitDataForTask property) transfer_learning() (larry._datasets._data.inVitroData method) (larry._datasets._in_vitro_dataset.inVitroDataset method) (larry._datasets.inVitroData method) transfer_learning_h5ad_path (larry._datasets._data.DataHandler property)

U

UMAP (larry._datasets._dimension_reduction.DimensionReduction property) (larry._datasets.DimensionReduction property) umap_transform() (larry._utils._model_evaluator.ModelEvaluator method) uniform (larry._datasets._anndata_path_manager.AnnDataPathManager property) (larry._datasets.AnnDataPathManager property)

URL (larry._datasets._url_path_interfaces.FormattedURLFile property) URLPathInterface (class in larry._datasets._url_path_interfaces) URLPaths (larry._datasets._data.DataHandler property)

V

var (larry._datasets._anndata_configuration.AnnDataConfiguration property) (larry._datasets._data.DataHandler property) (larry._datasets.AnnDataConfiguration property)

ViolinPlot (class in larry._analysis._growth_rate_grouped_violin_plot) vscores() (in module larry._datasets) (in module larry._datasets.klein_lab_pp_recipe) (in module larry._datasets.klein_lab_pp_recipe._vscores)

X

X (larry._datasets._anndata_configuration.AnnDataConfiguration property) (larry._datasets._data.DataHandler property) (larry._datasets.AnnDataConfiguration property) X0 (larry._utils._model_evaluator.ModelEvaluator property) X_clone (larry._datasets._anndata_configuration.AnnDataConfiguration property) (larry._datasets._data.DataHandler property) (larry._datasets.AnnDataConfiguration property) X_test (larry._datasets._split_data.SplitDataForTask property) (larry._datasets.SplitDataForTask property) X_test_pca (larry._datasets._split_data.SplitDataForTask property) (larry._datasets.SplitDataForTask property)

X_test_scaled (larry._datasets._split_data.SplitDataForTask property) (larry._datasets.SplitDataForTask property) X_test_umap (larry._datasets._split_data.SplitDataForTask property) (larry._datasets.SplitDataForTask property) X_train (larry._datasets._split_data.SplitDataForTask property) (larry._datasets.SplitDataForTask property) X_train_pca (larry._datasets._split_data.SplitDataForTask property) (larry._datasets.SplitDataForTask property) X_train_scaled (larry._datasets._split_data.SplitDataForTask property) (larry._datasets.SplitDataForTask property) X_train_umap (larry._datasets._split_data.SplitDataForTask property) (larry._datasets.SplitDataForTask property)

Y

y_pred (larry._utils._confusion_matrix.ConfusionMatrix property)

y_true (larry._utils._confusion_matrix.ConfusionMatrix property)