Index

Symbols

--adjacency command line option --cvae_init_lr command line option --cvae_input_scaler command line option --cvae_train_epoch command line option --diagnosis command line option, [1] --diameter command line option, [1] --fc_cutoff command line option --filter_cell command line option --filter_gene command line option --help command line option, [1] --hole_min_spots command line option, [1] --impute_diameter command line option, [1] --lambda_g command line option --lambda_g_range_k command line option --lambda_g_range_max command line option --lambda_g_range_min command line option --lambda_r command line option --lambda_r_range_k command line option --lambda_r_range_max command line option --lambda_r_range_min command line option --loc command line option, [1] --marker command line option --n_cores command line option --n_hv_gene command line option --n_marker_per_cmp command line option --n_pseudo_spot command line option --num_hidden_layer command line option --p_val_cutoff command line option --pct1_cutoff command line option --pct2_cutoff command line option

--preserve_shape command line option, [1] --prop command line option --pseudo_spot_max_cell command line option --pseudo_spot_min_cell command line option --query command line option, [1] --redo_de command line option --ref command line option --ref_anno command line option --seed command line option --seq_depth_scaler command line option --sortby_fc command line option --threshold command line option --use_batch_norm command line option --use_cvae command line option --use_fdr command line option --use_imputation command line option --use_spatial_pseudo command line option --verbose command line option --version command line option, [1] -a command line option -c command line option -h command line option, [1] -l command line option, [1] -m command line option -n command line option -p command line option -q command line option, [1] -r command line option -v command line option, [1]

A

adaptive_lasso() (in module local_fit_numba) admm_fit module

augment_sc() (in module cvae)

B

BIC_find_lambda_r_one_spot() (in module hyper_parameter_optimization) BIC_find_theta_subset_one_spot() (in module hyper_parameter_optimization)

build_CVAE() (in module cvae) build_CVAE_whole() (in module cvae)

C

calc_AIC_BIC() (in module hyper_parameter_optimization) calc_hv_numba() (in module local_fit_numba) calcHVBaseModelLoss() (in module hyper_parameter_optimization) calcRMSE() (in module utils) celltype2props() (in module cvae) check_decoder() (in module utils) check_numba() (in module utils) check_technique() (in module imputation) checkEarlyStop() (in module hyper_parameter_optimization) combine_spatial_spots() (in module cvae) command line option --adjacency --cvae_init_lr --cvae_input_scaler --cvae_train_epoch --diagnosis, [1] --diameter, [1] --fc_cutoff --filter_cell --filter_gene --help, [1] --hole_min_spots, [1] --impute_diameter, [1] --lambda_g --lambda_g_range_k --lambda_g_range_max --lambda_g_range_min --lambda_r --lambda_r_range_k --lambda_r_range_max --lambda_r_range_min --loc, [1] --marker --n_cores --n_hv_gene --n_marker_per_cmp --n_pseudo_spot --num_hidden_layer --p_val_cutoff --pct1_cutoff --pct2_cutoff --preserve_shape, [1] --prop --pseudo_spot_max_cell --pseudo_spot_min_cell --query, [1] --redo_de --ref --ref_anno --seed --seq_depth_scaler --sortby_fc --threshold --use_batch_norm --use_cvae --use_fdr --use_imputation --use_spatial_pseudo --verbose --version, [1] -a -c -h, [1] -l, [1] -m -n -p -q, [1] -r -v, [1]

config module construct_M_matrix() (in module imputation) create_grid() (in module imputation) cv_find_lambda_g() (in module hyper_parameter_optimization) cv_find_lambda_r() (in module hyper_parameter_optimization) cvae module CVAE_keras_model() (in module cvae) cvaeglrm module

D

defineColor() (in module diagnosis_plots) diagnosis_path (in module config) diagnosis_plots module

diagnosisCVAE() (in module diagnosis_plots) diagnosisParamsSpotwiseLambdarTuning() (in module diagnosis_plots) diagnosisParamsTuning() (in module diagnosis_plots) do_imputation() (in module imputation) do_random_walk() (in module imputation)

E

estimating_gamma_g() (in module model_fit)

F

fit_base_model() (in module model_fit) fit_base_model_plus_laplacian() (in module local_fit_numba)

fit_model_two_stage() (in module model_fit) fit_stage1_spotwise_lambda_r() (in module model_fit)

G

gamma (in module config)

generate_log_heavytail_array() (in module local_fit_numba) generate_pseudo_spots() (in module cvae)

H

hv_comb() (in module local_fit_numba) hv_wrapper() (in module local_fit_numba)

hyper_parameter_optimization module

I

identify_edges() (in module imputation) imputation module

impute_expression() (in module imputation) impute_spots_with_theta() (in module imputation) initialize_theta_grid_points() (in module imputation) is_docker() (in module config)

L

local_fit_numba module

M

main() (in module cvaeglrm) (in module imputation) min_sigma2 (in module config) min_theta (in module config) min_val (in module config) model_fit module module admm_fit config cvae cvaeglrm diagnosis_plots hyper_parameter_optimization imputation local_fit_numba model_fit parse_opt preprocess run_model utils version

N

numba_info() (in module utils)

O

objective_loss_theta() (in module local_fit_numba)

one_admm_fit() (in module admm_fit) optimize_one_theta() (in module local_fit_numba)

P

parse_opt module parseOpt() (in module imputation) (in module parse_opt) plot_imputation() (in module diagnosis_plots)

plotCVAELoss() (in module diagnosis_plots) preprocess module preprocess() (in module preprocess) print() (in module config)

R

RandomDisplacementBounds (class in local_fit_numba) rawInputUMAP() (in module diagnosis_plots) read_scRNA_data() (in module utils) read_spatial_data() (in module utils) reparameterTheta() (in module utils) reportRMSE() (in module utils)

rerun_DE() (in module utils) run_DE() (in module utils) run_DE_only() (in module utils) run_GLRM() (in module run_model) run_model module

S

sigma2_eps (in module config)

stepsize (local_fit_numba.RandomDisplacementBounds attribute)

T

total_size() (in module utils)

transferProps() (in module cvae)

U

update_sigma2() (in module local_fit_numba) update_theta() (in module local_fit_numba) usage() (in module imputation) (in module parse_opt)

utils module

V

version module

X

xmax (local_fit_numba.RandomDisplacementBounds attribute)

xmin (local_fit_numba.RandomDisplacementBounds attribute)