Index

A

aggregate_program_scores() (in module spatialperturb) (in module spatialperturb.signatures) assign_perturbations() (in module spatialperturb) (in module spatialperturb.pp)

available_benchmarks() (in module spatialperturb) (in module spatialperturb.benchmarks) available_datasets() (in module spatialperturb) (in module spatialperturb.datasets)

B

barcode_spread() (in module spatialperturb.pl) bootstrap_program_score_intervals() (in module spatialperturb) (in module spatialperturb.signatures) build_reference_programs() (in module spatialperturb) (in module spatialperturb.signatures)

build_signature_matrix() (in module spatialperturb) (in module spatialperturb.signatures) build_spatial_graph() (in module spatialperturb) (in module spatialperturb.gr)

C

calibrate_program_scores() (in module spatialperturb) (in module spatialperturb.signatures) collect_neighbors() (in module spatialperturb) (in module spatialperturb.gr)

compare_program_concordance() (in module spatialperturb) (in module spatialperturb.signatures)

D

DatasetCard (class in spatialperturb.datasets) dense_spatial_scatter() (in module spatialperturb) (in module spatialperturb.figurekit)

derive_perturbation_programs() (in module spatialperturb) (in module spatialperturb.signatures) differential_lr() (in module spatialperturb) (in module spatialperturb.tl)

E

ensure_spatialperturb_schema() (in module spatialperturb) (in module spatialperturb.schema)

F

fetch_dataset() (in module spatialperturb) (in module spatialperturb.datasets) fetch_dataset_command() (in module spatialperturb.cli)

FigureKitError from_tables() (in module spatialperturb) (in module spatialperturb.io)

G

get_dataset_card() (in module spatialperturb) (in module spatialperturb.datasets)

I

intrinsic_de() (in module spatialperturb) (in module spatialperturb.tl)

L

list_benchmarks() (in module spatialperturb.cli) list_datasets() (in module spatialperturb.cli) load_demo_dataset() (in module spatialperturb) (in module spatialperturb.datasets)

load_public_dataset() (in module spatialperturb) (in module spatialperturb.datasets) lr_map() (in module spatialperturb.pl) lr_pairs() (in module spatialperturb.pl)

M

main() (in module spatialperturb.cli) module spatialperturb spatialperturb.benchmarks spatialperturb.cli spatialperturb.datasets spatialperturb.figurekit spatialperturb.gr spatialperturb.io spatialperturb.pl spatialperturb.pp spatialperturb.reports spatialperturb.schema spatialperturb.signatures spatialperturb.tl

N

neighbor_de() (in module spatialperturb) (in module spatialperturb.tl)

neighbor_program_scores() (in module spatialperturb) (in module spatialperturb.signatures)

O

own_vs_neighbor() (in module spatialperturb.pl)

P

PanelSpec (class in spatialperturb) (class in spatialperturb.figurekit) platform_concordance() (in module spatialperturb) (in module spatialperturb.pl) (in module spatialperturb.tl) power_curve() (in module spatialperturb) (in module spatialperturb.pl) (in module spatialperturb.tl)

prepare_dataset() (in module spatialperturb) (in module spatialperturb.datasets) prepare_dataset_command() (in module spatialperturb.cli) prepare_xenium_command() (in module spatialperturb.cli) program_redundancy_table() (in module spatialperturb) (in module spatialperturb.signatures)

Q

qc_perturbations() (in module spatialperturb) (in module spatialperturb.pp)

R

read_stereoseq() (in module spatialperturb) (in module spatialperturb.io) read_xenium() (in module spatialperturb) (in module spatialperturb.io) render_nature_methods_panels() (in module spatialperturb) (in module spatialperturb.figurekit) render_paper_figures() (in module spatialperturb) (in module spatialperturb.reports) render_paper_figures_command() (in module spatialperturb.cli) run_benchmark_command() (in module spatialperturb.cli)

run_core_benchmark() (in module spatialperturb) (in module spatialperturb.benchmarks) run_cross_platform_benchmark() (in module spatialperturb) (in module spatialperturb.benchmarks) run_nature_methods_breast_analysis() (in module spatialperturb) (in module spatialperturb.benchmarks) run_nature_methods_breast_analysis_command() (in module spatialperturb.cli) run_reference_benchmark_command() (in module spatialperturb.cli) run_reference_projection_benchmark() (in module spatialperturb) (in module spatialperturb.benchmarks)

S

save_panel() (in module spatialperturb) (in module spatialperturb.figurekit) schema_summary() (in module spatialperturb.schema) score_programs() (in module spatialperturb) (in module spatialperturb.signatures) set_publication_rcparams() (in module spatialperturb) (in module spatialperturb.figurekit) spatial_autocorrelation_scores() (in module spatialperturb) (in module spatialperturb.signatures) spatialperturb module spatialperturb.benchmarks module spatialperturb.cli module spatialperturb.datasets module spatialperturb.figurekit module

spatialperturb.gr module spatialperturb.io module spatialperturb.pl module spatialperturb.pp module spatialperturb.reports module spatialperturb.schema module spatialperturb.signatures module spatialperturb.tl module SpatialPerturbSchemaError, [1]

V

validate() (in module spatialperturb.cli) validate_reference_programs() (in module spatialperturb) (in module spatialperturb.signatures)

validate_spatialperturb_schema() (in module spatialperturb) (in module spatialperturb.schema) version() (in module spatialperturb.cli)