Index

_

__iter__() (hts.plate_data.plate_data.PlateData method) (hts.run.run.Run method) __str__() (hts.plate.plate.Plate method) (hts.plate_data.plate_data.PlateData method) (hts.plate_data.readout.Readout method) (hts.run.run.Run method)

_platelayout (hts.run.run.Run attribute) _protocol (hts.run.run.Run attribute) _qc (hts.run.run.Run attribute)

A

add_data() (hts.plate.plate.Plate method) (hts.plate_data.plate_data.PlateData method) add_data_from_data_frame() (hts.run.run.Run method)

add_meta_data() (hts.run.run.Run method) (in module hts.run.run_io) analysis() (hts.run.run.Run method)

C

calculate_control_normalized_signal() (hts.plate.plate.Plate method) calculate_linearly_normalized_signal() (hts.plate.plate.Plate method) calculate_local_ssmd() (hts.plate.plate.Plate method) (in module hts.data_tasks.data_normalization) calculate_net_fret() (hts.plate.plate.Plate method) calculate_normalization_by_division() (hts.plate.plate.Plate method) calculate_significance_compared_to_null_distribution() (hts.plate.plate.Plate method) chessboard_pattern() (in module hts.data_tasks.qc_knitr) classify_by_cutoff() (hts.plate.plate.Plate method) (in module hts.data_tasks.data_normalization) column_plate_name (in module hts.run.run_io) column_well (in module hts.run.run_io) columns_metas (in module hts.run.run_io) columns_readouts (in module hts.run.run_io) compare_plate_replicates() (in module hts.data_tasks.qc_knitr) config (hts.protocol.protocol.ProtocolTask attribute) convert_well_id_format() (in module hts.run.run_io) create() (hts.plate.plate.Plate method) (hts.plate_data.plate_data.PlateData class method) (hts.protocol.protocol.Protocol class method) (hts.protocol.protocol.ProtocolTask class method) (hts.run.run.Run class method)

create_csv() (hts.plate_data.plate_data.PlateData class method) (hts.plate_data.plate_layout.PlateLayout class method) create_envision_csv() (hts.plate_data.readout.Readout method) create_excel() (hts.plate_data.plate_data.PlateData class method) create_excel_multiple_plates_per_file() (hts.plate_data.plate_data.PlateData class method) create_from_config() (hts.run.run.Run class method) create_from_coordinate_tuple_dict() (hts.plate_data.plate_data.PlateData class method) create_from_csv_file() (hts.run.run.Run class method) create_from_envision() (hts.run.run.Run class method) create_insulin_csv() (hts.plate_data.readout.Readout method) create_pickle() (hts.plate_data.plate_data.PlateData class method) create_report() (in module hts.data_tasks.qc_knitr) (in module hts.data_tasks.qc_matplotlib) create_well_list() (hts.plate_data.data_issue.DataIssue class method) cross_validate_predictions() (hts.plate.plate.Plate method)

D

data (hts.plate_data.plate_data.PlateData attribute) (hts.plate_data.readout.Readout attribute) data_frame() (hts.run.run.Run property) data_frame_samples() (hts.run.run.Run property)

DataIssue (class in hts.plate_data.data_issue) delimiter (in module hts.run.run_io) detect_low_cell_viability() (in module hts.data_tasks.qc_detect_data_issues) do_task() (hts.run.run.Run method) dynamics() (in module hts.data_tasks.qc_knitr)

E

evaluate_well_value_prediction() (hts.plate.plate.Plate method)

experimenter (hts.run.run.Run attribute), [1]

F

file (hts.protocol.protocol.Protocol attribute) (in module hts.run.run_io) filter() (hts.plate.plate.Plate method) (hts.run.run.Run method)

flatten_data() (hts.plate.plate.Plate method) flatten_values() (hts.plate.plate.Plate method) flatten_wells() (hts.plate.plate.Plate method)

G

get_data() (hts.plate_data.plate_data.PlateData method) get_data_for_gaussian_process() (hts.plate.plate.Plate method) get_run_config_data() (hts.run.run.Run method)

get_tasks_by_tag() (hts.protocol.protocol.Protocol method) get_values() (hts.plate_data.plate_data.PlateData method) get_wells() (hts.plate_data.plate_data.PlateData method) gp_models() (hts.run.run.Run property)

H

heat_map() (in module hts.data_tasks.qc_knitr) heat_map_log10_mark_conditionally() (in module hts.data_tasks.qc_knitr) heat_map_mark_conditionally() (in module hts.data_tasks.qc_knitr) heat_map_multiple() (in module hts.data_tasks.qc_matplotlib) heat_map_multiple_gaussian_process_model() (in module hts.data_tasks.qc_matplotlib) heat_map_single() (in module hts.data_tasks.qc_matplotlib) heat_map_single_gaussian_process_model() (in module hts.data_tasks.qc_matplotlib) height (hts.plate.plate.Plate attribute) (hts.plate_data.plate_data.PlateData attribute) (hts.plate_data.readout.Readout attribute) (hts.run.run.Run attribute) hts (module) hts.conftest (module) hts.data_tasks (module) hts.data_tasks.data_normalization (module) hts.data_tasks.data_tasks (module) hts.data_tasks.qc_detect_data_issues (module)

hts.data_tasks.qc_knitr (module) hts.data_tasks.qc_matplotlib (module) hts.plate (module) hts.plate.plate (module) hts.plate_data (module) hts.plate_data.data_issue (module) hts.plate_data.meta_data (module) hts.plate_data.plate_data (module) hts.plate_data.plate_data_io (module) hts.plate_data.plate_layout (module) hts.plate_data.readout (module) hts.plate_data.readout_io (module) hts.protocol (module) hts.protocol.protocol (module) hts.run (module) hts.run.constants (module) hts.run.run (module) hts.run.run_io (module)

I

invert() (hts.plate_data.plate_layout.PlateLayout method)

K

knitr_header_setup() (in module hts.data_tasks.qc_knitr) knitr_subset() (in module hts.data_tasks.qc_knitr)

kolmogorov_smirnov() (in module hts.data_tasks.qc_knitr) kolmogorov_smirnov_estimated() (in module hts.data_tasks.qc_knitr)

L

layout_general_type (hts.plate_data.data_issue.DataIssue attribute) (hts.plate_data.plate_layout.PlateLayout attribute)

M

map_config_file_definition() (hts.run.run.Run class method) map_coordinates() (hts.plate.plate.Plate method) mean_value_across_plates() (in module hts.data_tasks.qc_knitr) merged_replicates() (in module hts.run.run)

merger_add_data_from_data_frame() (hts.run.run.Run method) merger_rank_samples() (hts.run.run.Run method) merger_summarize_statistical_significance() (hts.run.run.Run method) MetaData (class in hts.plate_data.meta_data) method (hts.protocol.protocol.ProtocolTask attribute)

N

name (hts.plate.plate.Plate attribute) (hts.protocol.protocol.Protocol attribute) (hts.protocol.protocol.ProtocolTask attribute) (hts.run.run.Run attribute)

net_qc (hts.run.run.Run attribute)

P

perform_qc() (in module hts.data_tasks.qc_knitr) perform_task() (in module hts.data_tasks.data_tasks) Plate (class in hts.plate.plate) plate_layout() (in module hts.data_tasks.qc_knitr) plate_layout_name (in module hts.run.run_io), [1] plate_name (in module hts.run.run_io), [1] PlateData (class in hts.plate_data.plate_data)

PlateLayout (class in hts.plate_data.plate_layout) plates (hts.run.run.Run attribute) preprocess() (hts.plate.plate.Plate method) (hts.run.run.Run method) Protocol (class in hts.protocol.protocol) protocol() (hts.run.run.Run method) ProtocolTask (class in hts.protocol.protocol) pytest_runtest_setup() (in module hts.conftest)

Q

qc() (hts.run.run.Run method)

R

randomize_values() (hts.plate.plate.Plate method) raw_qc (hts.run.run.Run attribute) read_csv() (in module hts.plate_data.plate_data_io) (in module hts.run.run_io) read_envision_csv() (in module hts.plate_data.readout_io) read_excel() (in module hts.plate_data.plate_data_io) read_insulin_csv() (in module hts.plate_data.readout_io)

Readout (class in hts.plate_data.readout) readouts (in module hts.run.run_io), [1] rename_pd_columns() (in module hts.run.run_io) replicate_correlation() (in module hts.data_tasks.qc_knitr) replicate_correlation_robust() (in module hts.data_tasks.qc_knitr) Run (class in hts.run.run) run (in module hts.run.run_io)

S

sample_replicate_count (hts.plate_data.data_issue.DataIssue attribute) (hts.plate_data.plate_layout.PlateLayout attribute) send_mail() (in module hts.run.run) serialize_as_csv_one_row_per_well() (in module hts.run.run_io) serialize_as_pandas() (in module hts.run.run_io) serialize_run_for_r() (in module hts.run.run_io)

shapiro_wilk_normality_test() (in module hts.data_tasks.qc_knitr) slice_multiple_gaussian_process_model() (in module hts.data_tasks.qc_matplotlib) slice_single_gaussian_process_model() (in module hts.data_tasks.qc_matplotlib) smoothed_histogram() (in module hts.data_tasks.qc_knitr) smoothed_histogram_sample_type() (in module hts.data_tasks.qc_knitr) ssmd() (in module hts.data_tasks.qc_knitr) subtract_readouts() (hts.plate.plate.Plate method)

T

tags (hts.plate_data.plate_data.PlateData attribute) (hts.protocol.protocol.ProtocolTask attribute) tasks (hts.protocol.protocol.Protocol attribute)

time_course() (in module hts.data_tasks.qc_knitr) translate_coordinate_humanreadable() (in module hts.plate.plate) translate_humanreadable_coordinate() (in module hts.plate.plate) type (hts.protocol.protocol.ProtocolTask attribute)

U

un_flatten_data() (hts.plate.plate.Plate method)

W

well_name (in module hts.run.run_io), [1] width (hts.plate.plate.Plate attribute) (hts.plate_data.plate_data.PlateData attribute) (hts.plate_data.readout.Readout attribute) (hts.run.run.Run attribute)

wrap_knitr_chunk() (in module hts.data_tasks.qc_knitr) write() (hts.plate.plate.Plate method) (hts.plate_data.plate_data.PlateData method) (hts.protocol.protocol.Protocol method) (hts.run.run.Run method)

Z

z_factor() (in module hts.data_tasks.qc_knitr)

z_prime_factor() (in module hts.data_tasks.qc_knitr)