Index

_

__init__() (scspecies.models.Decoder method) (scspecies.models.Encoder_inner method) (scspecies.models.Encoder_outer method) (scspecies.models.Library_encoder method) (scspecies.models.make_act_bounded method) (scspecies.models.Progress_Bar method) (scspecies.models.scSpecies method), [1], [2], [3] (scspecies.preprocessing.create_mdata method), [1]

__new__() (scspecies.models.Decoder static method) (scspecies.models.Encoder_inner static method) (scspecies.models.Encoder_outer static method) (scspecies.models.Library_encoder static method) (scspecies.models.make_act_bounded static method)

A

average_slices() (scspecies.models.scSpecies static method), [1]

C

calc_nlog_likelihood() (scspecies.models.Decoder method) color_str() (in module scspecies.models) compute_lib_prior_params() (scspecies.preprocessing.create_mdata static method), [1]

compute_logfold_change() (scspecies.models.scSpecies method), [1], [2] create_directory() (scspecies.models.scSpecies method), [1] create_mdata (class in scspecies.preprocessing), [1] create_structure() (in module scspecies.models)

D

decode() (scspecies.models.Decoder method) decode_homologous() (scspecies.models.Decoder method)

Decoder (class in scspecies.models) download_datasets() (in module scspecies.preprocessing), [1]

E

encode() (scspecies.models.Encoder_inner method) (scspecies.models.Library_encoder method) (scspecies.models.scSpecies method), [1], [2]

encode_batch_labels() (scspecies.preprocessing.create_mdata static method) Encoder_inner (class in scspecies.models) Encoder_outer (class in scspecies.models)

F

filter_cells() (scspecies.preprocessing.create_mdata static method) filter_outliers() (scspecies.models.scSpecies static method), [1] format_number() (scspecies.models.Progress_Bar static method) forward() (scspecies.models.Decoder method) (scspecies.models.Encoder_inner method) (scspecies.models.Encoder_outer method) (scspecies.models.Library_encoder method) (scspecies.models.make_act_bounded method)

G

generate_homologous_samples() (scspecies.models.scSpecies method), [1], [2] get_batch() (scspecies.models.scSpecies method), [1]

get_key() (in module scspecies.preprocessing) get_representation() (scspecies.models.scSpecies method), [1], [2]

H

hmu() (scspecies.models.scSpecies method), [1]

I

initialize() (scspecies.models.scSpecies method), [1], [2]

is_bright() (in module scspecies.plot)

L

label_transfer_acc() (in module scspecies.plot), [1] Library_encoder (class in scspecies.models) load() (scspecies.models.scSpecies method), [1], [2]

load_and_filter_pathways() (in module scspecies.plot), [1] log_alpha (scspecies.models.Decoder attribute) log_sig (scspecies.models.Encoder_inner attribute) (scspecies.models.Library_encoder attribute)

M

make_act_bounded (class in scspecies.models) map_homologs() (in module scspecies.preprocessing) map_homologs_silent() (in module scspecies.preprocessing) mode_histogram() (scspecies.models.scSpecies static method), [1] model (scspecies.models.Decoder attribute) (scspecies.models.Encoder_inner attribute) (scspecies.models.Encoder_outer attribute) (scspecies.models.Library_encoder attribute)

module scspecies scspecies.models scspecies.plot, [1] scspecies.preprocessing, [1] most_frequent() (scspecies.models.scSpecies static method), [1] mu (scspecies.models.Encoder_inner attribute) (scspecies.models.Library_encoder attribute) mu_add (scspecies.models.Library_encoder attribute)

N

neighbors_workaround() (in module scspecies.models), [1], [2]

O

opt() (scspecies.models.scSpecies method), [1]

P

pi_nlogit (scspecies.models.Decoder attribute) pkl() (scspecies.models.scSpecies method), [1] plot_2D_representation() (in module scspecies.plot), [1] plot_lfc() (in module scspecies.plot), [1] plot_lfc_comparison() (in module scspecies.plot), [1]

plot_prototype_sim_heatmap() (in module scspecies.plot), [1] plot_similarity() (in module scspecies.plot), [1] pred_labels_nns_hom_genes() (scspecies.preprocessing.create_mdata method) Progress_Bar (class in scspecies.models) progressive_moving_average() (in module scspecies.plot) pth() (scspecies.models.scSpecies method), [1]

R

ret_pred_df() (scspecies.models.scSpecies method), [1], [2] ret_sign() (in module scspecies.plot) (scspecies.models.Progress_Bar method)

return_mdata() (scspecies.preprocessing.create_mdata method), [1] return_palette() (in module scspecies.plot), [1] return_similarity_df() (scspecies.models.scSpecies method), [1], [2] rho_pre (scspecies.models.Decoder attribute)

S

sampling_dist (scspecies.models.Encoder_inner attribute) (scspecies.models.Library_encoder attribute) save() (scspecies.models.scSpecies method), [1], [2] save_mdata() (scspecies.models.scSpecies method), [1], [2] scspecies module scSpecies (class in scspecies.models), [1], [2] scspecies.models module

scspecies.plot module, [1] scspecies.preprocessing module, [1] set_random_seed() (in module scspecies.preprocessing), [1] setup_target_adata() (scspecies.preprocessing.create_mdata method), [1] similarity_metric() (scspecies.models.scSpecies method), [1], [2] similarity_metric_on_latent_space() (scspecies.models.scSpecies method), [1], [2] subset_to_hvg() (scspecies.preprocessing.create_mdata static method), [1]

T

train_context() (scspecies.models.scSpecies method), [1], [2] train_target() (scspecies.models.scSpecies method), [1], [2]

transfer_labels_cell() (scspecies.models.scSpecies method), [1], [2] transfer_labels_data() (scspecies.models.scSpecies method), [1], [2] translate_gene_list() (scspecies.preprocessing.create_mdata method)

U

update() (scspecies.models.Progress_Bar method)

update_param() (scspecies.models.scSpecies static method), [1]