Index

A

AccessibilityConfig (class in lbfextract.transcription_factor_analysis.schemas) action_check_task_status() (lbfextract.fextract.tui.app.FextractApp method) action_toggle_processes_pane() (lbfextract.fextract.tui.app.FextractApp method)

action_toggle_tree() (lbfextract.fextract.tui.app.FextractApp method) annotation_center_line (lbfextract.fextract_batch_coverage.schemas.PlotConfig attribute) AppExtraConfig (class in lbfextract.fextract.schemas) apply_savgol (lbfextract.fextract_batch_coverage.schemas.PlotConfig attribute)

B

bedfile (lbfextract.fextract.schemas.SignalSummarizer attribute) BINDINGS (lbfextract.fextract.tui.app.FextractApp attribute)

bottom (lbfextract.fextract_batch_coverage.schemas.PlotConfig attribute) bubble (lbfextract.fextract.tui.my_directory_tree.DirectoryTree.FileClick attribute)

C

calculate_reference_distribution() (in module lbfextract.fextract.cli_lib) (in module lbfextract.fextract_fragment_length_distribution.plugin) can_focus (lbfextract.fextract.tui.app.Welcome attribute) (lbfextract.fextract.tui.my_directory_tree.DirectoryTree attribute) can_focus_children (lbfextract.fextract.tui.app.Welcome attribute) (lbfextract.fextract.tui.my_directory_tree.DirectoryTree attribute) check_conda_env_was_installed() (in module lbfextract) check_signal_type_compatibility() (lbfextract.transcription_factor_analysis.loaders.ResultsLoader method) Chromosome (lbfextract.fextract.signal_transformer.GenomiIntervalDataFrameRow attribute) CliHook (class in lbfextract.fextract.cli_lib) (class in lbfextract.fextract_batch_coverage.plugin) (class in lbfextract.fextract_entropy.plugin) (class in lbfextract.fextract_fragment_length_distribution.plugin) (class in lbfextract.fextract_fragment_length_distribution_in_batch.plugin) (class in lbfextract.fextract_fragment_length_ratios.plugin) (class in lbfextract.fextract_relative_entropy_to_flanking.plugin)

CliHookExtractCoverage (class in lbfextract.fextract.cli_lib) color (lbfextract.fextract_batch_coverage.schemas.PlotConfig attribute) compose() (lbfextract.fextract.tui.app.FextractApp method) (lbfextract.fextract.tui.app.Welcome method) Config (class in lbfextract.fextract.schemas) cores (lbfextract.fextract.schemas.AppExtraConfig attribute) (lbfextract.fextract.schemas.ReadFetcherConfig attribute) correlation_map_plot() (in module lbfextract.plotting_lib.plotting_functions) create_heatmap_bed_per_position() (in module lbfextract.plotting_lib.plotting_functions) create_masked_corr_matrix_plot() (in module lbfextract.plotting_lib.plotting_functions) create_path() (in module lbfextract.transcription_factor_analysis.differential_signal_analysis) CSS_PATH (lbfextract.fextract.tui.app.FextractApp attribute) ctx (lbfextract.fextract.schemas.AppExtraConfig attribute) custom_warning_handler() (in module lbfextract)

D

DEFAULT_CSS (lbfextract.fextract.tui.app.Welcome attribute) DiffSignalAnalysis (class in lbfextract.transcription_factor_analysis.differential_signal_analysis)

DirectoryTree (class in lbfextract.fextract.tui.my_directory_tree) DirectoryTree.FileClick (class in lbfextract.fextract.tui.my_directory_tree) DirEntry (class in lbfextract.fextract.tui.my_directory_tree)

E

End (lbfextract.fextract.signal_transformer.GenomiIntervalDataFrameRow attribute) end (lbfextract.transcription_factor_analysis.schemas.AccessibilityConfig attribute)

extra_bases (lbfextract.fextract.schemas.ReadFetcherConfig attribute) extract_coverage() (in module lbfextract.fextract_batch_coverage.plugin)

F

F (lbfextract.fextract.schemas.ReadFetcherConfig attribute) f (lbfextract.fextract.schemas.ReadFetcherConfig attribute) fetch_reads() (lbfextract.fextract.lib.FextractHooks method) (lbfextract.fextract_batch_coverage.plugin.FextractHooks method) (lbfextract.fextract_fragment_length_distribution_in_batch.plugin.FextractHooks method) FextractApp (class in lbfextract.fextract.tui.app) FextractHooks (class in lbfextract.fextract.lib) (class in lbfextract.fextract_batch_coverage.plugin) (class in lbfextract.fextract_entropy.plugin) (class in lbfextract.fextract_fragment_length_distribution.plugin) (class in lbfextract.fextract_fragment_length_distribution_in_batch.plugin) (class in lbfextract.fextract_fragment_length_ratios.plugin) (class in lbfextract.fextract_relative_entropy_to_flanking.plugin)

flanking (lbfextract.fextract_batch_coverage.schemas.PlotConfig attribute) flanking_region_window (lbfextract.fextract.schemas.ReadFetcherConfig attribute) flip_based_on_strand (lbfextract.fextract.schemas.SingleSignalTransformerConfig attribute) (lbfextract.fextract_fragment_length_distribution.schemas.SingleSignalTransformerConfig attribute) FragmentLengthDistribution (class in lbfextract.fextract.signal_transformer)

G

gc_correction (lbfextract.fextract.schemas.SingleSignalTransformerConfig attribute) (lbfextract.fextract_fragment_length_distribution.schemas.SingleSignalTransformerConfig attribute) general_font_size (lbfextract.fextract_batch_coverage.schemas.PlotConfig attribute) generate_bool_element() (in module lbfextract.fextract.tui.app) generate_form_from_command() (in module lbfextract.fextract.tui.app) generate_path_element() (in module lbfextract.fextract.tui.app) generate_sample_sheet() (lbfextract.transcription_factor_analysis.loaders.ResultsLoader method) generate_static() (in module lbfextract.fextract.tui.app) generate_time_stamp() (in module lbfextract.transcription_factor_analysis.utils) GenomiIntervalDataFrameRow (class in lbfextract.fextract.signal_transformer) get_accessibility() (lbfextract.transcription_factor_analysis.loaders.ResultsLoader method) get_chromatin_accessibility_coverage() (in module lbfextract.transcription_factor_analysis.accessibility_extraction) get_chromatin_accessibility_entropy() (in module lbfextract.transcription_factor_analysis.accessibility_extraction) get_command() (lbfextract.fextract.cli_lib.CliHook method) (lbfextract.fextract.cli_lib.CliHookExtractCoverage method) (lbfextract.fextract_batch_coverage.plugin.CliHook method) (lbfextract.fextract_entropy.plugin.CliHook method) (lbfextract.fextract_fragment_length_distribution.plugin.CliHook method) (lbfextract.fextract_fragment_length_distribution_in_batch.plugin.CliHook method) (lbfextract.fextract_fragment_length_ratios.plugin.CliHook method) (lbfextract.fextract_relative_entropy_to_flanking.plugin.CliHook method)

get_element_id() (in module lbfextract.fextract.tui.app) get_enrichment() (lbfextract.transcription_factor_analysis.differential_signal_analysis.DiffSignalAnalysis static method) get_minus_one_indices() (lbfextract.fextract.signal_transformer.WPSCoverage method) get_output_folder() (lbfextract.transcription_factor_analysis.differential_signal_analysis.DiffSignalAnalysis method) get_peaks() (in module lbfextract.fextract.cli_lib) (in module lbfextract.fextract_fragment_length_distribution.plugin) get_position_coefficient() (in module lbfextract.fextract_fragment_length_distribution.plugin) get_relative_start_end() (lbfextract.fextract.signal_transformer.TFBSCoverageAroundDyads method) (lbfextract.fextract_fragment_length_distribution.signal_summarizers.TfbsFragmentLengthDistribution method) (lbfextract.fextract_fragment_length_distribution.signal_summarizers.TfbsFragmentLengthDistributionDyad method) (lbfextract.fextract_fragment_length_distribution.signal_summarizers.TfbsFragmentLengthDistributionMiddleNPoints method) (lbfextract.fextract_fragment_length_distribution.signal_summarizers.TfbsFragmentLengthDistributionMiddlePoint method) get_res_df_polars() (lbfextract.transcription_factor_analysis.loaders.ResultsLoader method) get_state() (in module lbfextract.transcription_factor_analysis.differential_signal_analysis)

I

identity() (in module lbfextract.fextract_batch_coverage.plugin) (in module lbfextract.fextract_fragment_length_distribution_in_batch.plugin)

IntervalIterator (class in lbfextract.fextract_batch_coverage.plugin) IntervalIteratorFld (class in lbfextract.fextract_fragment_length_distribution_in_batch.plugin) is_dir (lbfextract.fextract.tui.my_directory_tree.DirEntry attribute)

L

lbfextract module lbfextract.fextract module lbfextract.fextract.cli_lib module lbfextract.fextract.lib module lbfextract.fextract.schemas module lbfextract.fextract.signal_transformer module lbfextract.fextract.tui.app module lbfextract.fextract.tui.my_directory_tree module lbfextract.fextract_batch_coverage module lbfextract.fextract_batch_coverage.plugin module lbfextract.fextract_batch_coverage.schemas module lbfextract.fextract_entropy module lbfextract.fextract_entropy.plugin module lbfextract.fextract_fragment_length_distribution module lbfextract.fextract_fragment_length_distribution.plugin module lbfextract.fextract_fragment_length_distribution.schemas module lbfextract.fextract_fragment_length_distribution.signal_summarizers module

lbfextract.fextract_fragment_length_distribution_in_batch module lbfextract.fextract_fragment_length_distribution_in_batch.plugin module lbfextract.fextract_fragment_length_ratios module lbfextract.fextract_fragment_length_ratios.plugin module lbfextract.fextract_relative_entropy_to_flanking module lbfextract.fextract_relative_entropy_to_flanking.plugin module lbfextract.plotting_lib module lbfextract.plotting_lib.plotting_functions module lbfextract.transcription_factor_analysis module lbfextract.transcription_factor_analysis.accessibility_extraction module lbfextract.transcription_factor_analysis.differential_signal_analysis module lbfextract.transcription_factor_analysis.loaders module lbfextract.transcription_factor_analysis.schemas module lbfextract.transcription_factor_analysis.utils module LbfextractInvalidConfigError load() (lbfextract.transcription_factor_analysis.loaders.ResultsLoader method) load_checks() (in module lbfextract.fextract.cli_lib) load_directory() (lbfextract.fextract.tui.my_directory_tree.DirectoryTree method) load_fetched_reads() (lbfextract.fextract.lib.FextractHooks method) (lbfextract.fextract_batch_coverage.plugin.FextractHooks method) load_sample_sheet() (lbfextract.transcription_factor_analysis.loaders.ResultsLoader method)

M

max_fragment_length (lbfextract.fextract.schemas.SingleSignalTransformerConfig attribute) (lbfextract.fextract_fragment_length_distribution.schemas.SingleSignalTransformerConfig attribute) min_fragment_length (lbfextract.fextract.schemas.SingleSignalTransformerConfig attribute) (lbfextract.fextract_fragment_length_distribution.schemas.SingleSignalTransformerConfig attribute) module lbfextract lbfextract.fextract lbfextract.fextract.cli_lib lbfextract.fextract.lib lbfextract.fextract.schemas lbfextract.fextract.signal_transformer lbfextract.fextract.tui.app lbfextract.fextract.tui.my_directory_tree lbfextract.fextract_batch_coverage lbfextract.fextract_batch_coverage.plugin lbfextract.fextract_batch_coverage.schemas lbfextract.fextract_entropy lbfextract.fextract_entropy.plugin lbfextract.fextract_fragment_length_distribution lbfextract.fextract_fragment_length_distribution.plugin lbfextract.fextract_fragment_length_distribution.schemas lbfextract.fextract_fragment_length_distribution.signal_summarizers lbfextract.fextract_fragment_length_distribution_in_batch lbfextract.fextract_fragment_length_distribution_in_batch.plugin lbfextract.fextract_fragment_length_ratios lbfextract.fextract_fragment_length_ratios.plugin lbfextract.fextract_relative_entropy_to_flanking lbfextract.fextract_relative_entropy_to_flanking.plugin lbfextract.plotting_lib lbfextract.plotting_lib.plotting_functions lbfextract.transcription_factor_analysis lbfextract.transcription_factor_analysis.accessibility_extraction lbfextract.transcription_factor_analysis.differential_signal_analysis lbfextract.transcription_factor_analysis.loaders lbfextract.transcription_factor_analysis.schemas lbfextract.transcription_factor_analysis.utils

N

n (lbfextract.fextract.schemas.SingleSignalTransformerConfig attribute) (lbfextract.fextract_fragment_length_distribution.schemas.SingleSignalTransformerConfig attribute) n_binding_sites (lbfextract.fextract.schemas.ReadFetcherConfig attribute) n_bins_len (lbfextract.fextract_fragment_length_distribution.schemas.SingleSignalTransformerConfig attribute)

n_bins_pos (lbfextract.fextract_fragment_length_distribution.schemas.SingleSignalTransformerConfig attribute) name (lbfextract.fextract.tui.my_directory_tree.DirectoryTree.FileClick attribute) namespace (lbfextract.fextract.tui.my_directory_tree.DirectoryTree.FileClick attribute) no_dispatch (lbfextract.fextract.tui.my_directory_tree.DirectoryTree.FileClick attribute) normalize_df() (lbfextract.transcription_factor_analysis.loaders.ResultsLoader method)

O

on_button_pressed() (lbfextract.fextract.tui.app.FextractApp method) on_checkbox_changed() (lbfextract.fextract.tui.app.FextractApp method) on_directory_tree_file_click() (lbfextract.fextract.tui.app.FextractApp method) on_input_changed() (lbfextract.fextract.tui.app.FextractApp method)

on_mount() (lbfextract.fextract.tui.my_directory_tree.DirectoryTree method) on_styles_updated() (lbfextract.fextract.tui.my_directory_tree.DirectoryTree method) on_tree_control_node_selected() (lbfextract.fextract.tui.my_directory_tree.DirectoryTree method) open_yml() (in module lbfextract.fextract.cli_lib) optimize_tensor_subsampling() (in module lbfextract.fextract_fragment_length_distribution_in_batch.plugin)

P

parse_indices() (in module lbfextract.transcription_factor_analysis.differential_signal_analysis) path (lbfextract.fextract.tui.my_directory_tree.DirEntry attribute) peaks (lbfextract.fextract.schemas.SingleSignalTransformerConfig attribute) (lbfextract.fextract_fragment_length_distribution.schemas.SingleSignalTransformerConfig attribute) PeterUlzCoverage (class in lbfextract.fextract.signal_transformer) PeterUlzFragmentLengthDistribution (class in lbfextract.fextract_fragment_length_distribution.signal_summarizers) plot_barplot_rejected_per_group() (lbfextract.transcription_factor_analysis.differential_signal_analysis.DiffSignalAnalysis method) plot_coverage() (lbfextract.transcription_factor_analysis.differential_signal_analysis.DiffSignalAnalysis method) plot_fragment_length_distribution() (in module lbfextract.plotting_lib.plotting_functions) plot_heatmap_diff_active_gi() (in module lbfextract.plotting_lib.plotting_functions) plot_heatmap_kde_amplitude() (in module lbfextract.plotting_lib.plotting_functions) plot_heatmap_signal_batch() (in module lbfextract.plotting_lib.plotting_functions)

plot_signal() (in module lbfextract.plotting_lib.plotting_functions) (lbfextract.fextract.lib.FextractHooks method) (lbfextract.fextract_batch_coverage.plugin.FextractHooks method) (lbfextract.fextract_entropy.plugin.FextractHooks method) (lbfextract.fextract_fragment_length_distribution.plugin.FextractHooks method) (lbfextract.fextract_fragment_length_distribution_in_batch.plugin.FextractHooks method) (lbfextract.fextract_fragment_length_ratios.plugin.FextractHooks method) (lbfextract.fextract_relative_entropy_to_flanking.plugin.FextractHooks method) plot_signal_batch() (in module lbfextract.plotting_lib.plotting_functions) PlotConfig (class in lbfextract.fextract_batch_coverage.schemas) possible_signal_transformers (lbfextract.fextract.schemas.SingleSignalTransformerConfig attribute) (lbfextract.fextract_fragment_length_distribution.schemas.SingleSignalTransformerConfig attribute) pressed_botton (lbfextract.fextract.tui.app.FextractApp attribute)

R

read_end (lbfextract.fextract.schemas.SingleSignalTransformerConfig attribute) (lbfextract.fextract_fragment_length_distribution.schemas.SingleSignalTransformerConfig attribute) read_start (lbfextract.fextract.schemas.SingleSignalTransformerConfig attribute) (lbfextract.fextract_fragment_length_distribution.schemas.SingleSignalTransformerConfig attribute) ReadFetcherConfig (class in lbfextract.fextract.schemas) reads_per_interval (lbfextract.fextract.signal_transformer.GenomiIntervalDataFrameRow attribute)

register_signal_type() (lbfextract.transcription_factor_analysis.loaders.ResultsLoader class method) remove_outliers() (in module lbfextract.transcription_factor_analysis.utils) render_node() (lbfextract.fextract.tui.my_directory_tree.DirectoryTree method) render_tree_label() (lbfextract.fextract.tui.my_directory_tree.DirectoryTree method) ResultsLoader (class in lbfextract.transcription_factor_analysis.loaders) run() (lbfextract.transcription_factor_analysis.differential_signal_analysis.DiffSignalAnalysis method) run_command() (lbfextract.fextract.tui.app.FextractApp method)

S

save_fetched_reads() (lbfextract.fextract.lib.FextractHooks method) (lbfextract.fextract_batch_coverage.plugin.FextractHooks method) save_results() (lbfextract.transcription_factor_analysis.differential_signal_analysis.DiffSignalAnalysis method) save_signal() (lbfextract.fextract.lib.FextractHooks method) (lbfextract.fextract_batch_coverage.plugin.FextractHooks method) (lbfextract.fextract_fragment_length_distribution.plugin.FextractHooks method) (lbfextract.fextract_fragment_length_distribution_in_batch.plugin.FextractHooks method) savgol_polyorder (lbfextract.fextract_batch_coverage.schemas.PlotConfig attribute) savgol_window_length (lbfextract.fextract_batch_coverage.schemas.PlotConfig attribute) schema (lbfextract.fextract.schemas.Config attribute) (lbfextract.fextract.schemas.ReadFetcherConfig attribute) (lbfextract.fextract.schemas.SignalSummarizer attribute) (lbfextract.fextract.schemas.SingleSignalTransformerConfig attribute) (lbfextract.fextract_batch_coverage.schemas.PlotConfig attribute) (lbfextract.fextract_fragment_length_distribution.schemas.SingleSignalTransformerConfig attribute) (lbfextract.transcription_factor_analysis.schemas.AccessibilityConfig attribute) Scrollview() (in module lbfextract.fextract.tui.app)

sender (lbfextract.fextract.tui.my_directory_tree.DirectoryTree.FileClick attribute) set_signal_summarizer() (lbfextract.fextract_batch_coverage.plugin.IntervalIterator method) set_signal_transformer() (lbfextract.fextract_batch_coverage.plugin.IntervalIterator method) (lbfextract.fextract_fragment_length_distribution_in_batch.plugin.IntervalIteratorFld method) show_tree (lbfextract.fextract.tui.app.FextractApp attribute) signal_transformer (lbfextract.fextract.schemas.SingleSignalTransformerConfig attribute) (lbfextract.fextract_fragment_length_distribution.schemas.SingleSignalTransformerConfig attribute) signal_types (lbfextract.transcription_factor_analysis.loaders.ResultsLoader attribute) SignalSummarizer (class in lbfextract.fextract.schemas) signed_log2() (in module lbfextract.transcription_factor_analysis.differential_signal_analysis) SingleSignalTransformerConfig (class in lbfextract.fextract.schemas) (class in lbfextract.fextract_fragment_length_distribution.schemas) Start (lbfextract.fextract.signal_transformer.GenomiIntervalDataFrameRow attribute) start (lbfextract.transcription_factor_analysis.schemas.AccessibilityConfig attribute) subsample (lbfextract.fextract_fragment_length_distribution.schemas.SingleSignalTransformerConfig attribute) subsample_fragment_lengths() (in module lbfextract.fextract_fragment_length_distribution.plugin) (in module lbfextract.fextract_fragment_length_distribution_in_batch.plugin) summarization_method (lbfextract.fextract.schemas.SignalSummarizer attribute)

T

tag (lbfextract.fextract.schemas.SingleSignalTransformerConfig attribute) (lbfextract.fextract_fragment_length_distribution.schemas.SingleSignalTransformerConfig attribute) tf_to_annotate (lbfextract.fextract_batch_coverage.schemas.PlotConfig attribute) TFBSCoverage (class in lbfextract.fextract.signal_transformer) TFBSCoverageAroundDyads (class in lbfextract.fextract.signal_transformer) TfbsFragmentLengthDistribution (class in lbfextract.fextract_fragment_length_distribution.signal_summarizers) TfbsFragmentLengthDistributionDyad (class in lbfextract.fextract_fragment_length_distribution.signal_summarizers) TfbsFragmentLengthDistributionMiddleNPoints (class in lbfextract.fextract_fragment_length_distribution.signal_summarizers) TfbsFragmentLengthDistributionMiddlePoint (class in lbfextract.fextract_fragment_length_distribution.signal_summarizers) TFBSMiddlePointCoverage (class in lbfextract.fextract.signal_transformer) TFBSNmiddlePointCoverage (class in lbfextract.fextract.signal_transformer) TFBSSlidingWindowCoverage (class in lbfextract.fextract.signal_transformer) time (lbfextract.fextract.tui.my_directory_tree.DirectoryTree.FileClick attribute) title_font_size (lbfextract.fextract_batch_coverage.schemas.PlotConfig attribute)

to_dict() (lbfextract.fextract.schemas.Config method) top (lbfextract.fextract_batch_coverage.schemas.PlotConfig attribute) transform_all_intervals() (lbfextract.fextract.lib.FextractHooks method) (lbfextract.fextract_batch_coverage.plugin.FextractHooks method) (lbfextract.fextract_entropy.plugin.FextractHooks method) (lbfextract.fextract_fragment_length_distribution.plugin.FextractHooks method) (lbfextract.fextract_fragment_length_distribution_in_batch.plugin.FextractHooks method) (lbfextract.fextract_fragment_length_ratios.plugin.FextractHooks method) (lbfextract.fextract_relative_entropy_to_flanking.plugin.FextractHooks method) transform_reads() (lbfextract.fextract.lib.FextractHooks method) transform_single_intervals() (lbfextract.fextract.lib.FextractHooks method) (lbfextract.fextract_batch_coverage.plugin.FextractHooks method) (lbfextract.fextract_fragment_length_distribution.plugin.FextractHooks method) (lbfextract.fextract_fragment_length_distribution_in_batch.plugin.FextractHooks method)

V

validate_nominator_denominator() (in module lbfextract.fextract_fragment_length_ratios.plugin)

verbose (lbfextract.fextract.tui.my_directory_tree.DirectoryTree.FileClick attribute)

W

w (lbfextract.fextract_fragment_length_distribution.schemas.SingleSignalTransformerConfig attribute) Welcome (class in lbfextract.fextract.tui.app) window (lbfextract.fextract.schemas.ReadFetcherConfig attribute)

window_center (lbfextract.fextract_batch_coverage.schemas.PlotConfig attribute) window_size (lbfextract.fextract.schemas.SingleSignalTransformerConfig attribute) WPSCoverage (class in lbfextract.fextract.signal_transformer)

X

xlabel (lbfextract.fextract_batch_coverage.schemas.PlotConfig attribute)

Y

ylabel (lbfextract.fextract_batch_coverage.schemas.PlotConfig attribute)