Index

A

ALDEx2Model (class in sccoda.model.other_models) ALRModel_ttest (class in sccoda.model.other_models) ALRModel_wilcoxon (class in sccoda.model.other_models)

analyze() (sccoda.model.other_models.scdney_model method) ANCOMBCModel (class in sccoda.model.other_models) AncomModel (class in sccoda.model.other_models) attrs() (sccoda.util.result_classes.CAResult property)

B

b_w_from_abs_change() (in module sccoda.util.data_generation)

BetaBinomialModel (class in sccoda.model.other_models) boxplots() (in module sccoda.util.data_visualization)

C

CAResult (class in sccoda.util.result_classes) CLRModel (class in sccoda.model.other_models) CLRModel_ttest (class in sccoda.model.other_models) compare_parameters_to_truth() (sccoda.util.result_classes.CAResult method) complete_alpha_df() (sccoda.util.result_classes.CAResult method)

complete_beta_df() (sccoda.util.result_classes.CAResult method) CompositionalAnalysis (class in sccoda.util.comp_ana) CompositionalModel (class in sccoda.model.scCODA_model) counts_from_first() (in module sccoda.util.data_generation) credible_effects() (sccoda.util.result_classes.CAResult method)

D

DirichRegModel (class in sccoda.model.other_models)

distance_to_truth() (sccoda.util.result_classes.CAResult method)

E

eval_model() (sccoda.model.other_models.ALDEx2Model method) (sccoda.model.other_models.ALRModel_ttest method) (sccoda.model.other_models.ALRModel_wilcoxon method) (sccoda.model.other_models.ANCOMBCModel method) (sccoda.model.other_models.AncomModel method) (sccoda.model.other_models.BetaBinomialModel method) (sccoda.model.other_models.CLRModel method) (sccoda.model.other_models.CLRModel_ttest method) (sccoda.model.other_models.DirichRegModel method) (sccoda.model.other_models.HaberModel method) (sccoda.model.other_models.TTest method)

F

fit_model() (sccoda.model.other_models.ALDEx2Model method) (sccoda.model.other_models.ALRModel_ttest method) (sccoda.model.other_models.ALRModel_wilcoxon method) (sccoda.model.other_models.ANCOMBCModel method) (sccoda.model.other_models.AncomModel method) (sccoda.model.other_models.BetaBinomialModel method) (sccoda.model.other_models.CLRModel method) (sccoda.model.other_models.CLRModel_ttest method) (sccoda.model.other_models.DirichRegModel method) (sccoda.model.other_models.HaberModel method) (sccoda.model.other_models.TTest method)

from_pandas() (in module sccoda.util.cell_composition_data) from_scanpy() (in module sccoda.util.cell_composition_data) from_scanpy_dir() (in module sccoda.util.cell_composition_data) from_scanpy_list() (in module sccoda.util.cell_composition_data)

G

generate_case_control() (in module sccoda.util.data_generation) get_chains_after_burnin() (sccoda.model.other_models.SimpleModel method) (sccoda.model.scCODA_model.CompositionalModel method) (sccoda.model.scCODA_model.scCODAModel method)

get_y_hat() (sccoda.model.other_models.SimpleModel method) (sccoda.model.scCODA_model.scCODAModel method)

H

HaberModel (class in sccoda.model.other_models)

M

make_result() (sccoda.model.other_models.SimpleModel method) (sccoda.model.scCODA_model.CompositionalModel method) (sccoda.model.scCODA_model.scCODAModel method)

module sccoda

R

read_anndata_one_sample() (in module sccoda.util.cell_composition_data)

S

sample_hmc() (sccoda.model.other_models.SimpleModel method) (sccoda.model.scCODA_model.CompositionalModel method) (sccoda.model.scCODA_model.scCODAModel method) sample_hmc_da() (sccoda.model.other_models.SimpleModel method) (sccoda.model.scCODA_model.CompositionalModel method) (sccoda.model.scCODA_model.scCODAModel method) sample_nuts() (sccoda.model.other_models.SimpleModel method) (sccoda.model.scCODA_model.CompositionalModel method) (sccoda.model.scCODA_model.scCODAModel method) sample_size_estimate() (in module sccoda.util.helper_functions) sampling() (sccoda.model.other_models.SimpleModel method) (sccoda.model.scCODA_model.CompositionalModel method) (sccoda.model.scCODA_model.scCODAModel method)

save() (sccoda.util.result_classes.CAResult method) sccoda module scCODAModel (class in sccoda.model.scCODA_model) scdney_model (class in sccoda.model.other_models) set_fdr() (sccoda.util.result_classes.CAResult method) SimpleModel (class in sccoda.model.other_models) sparse_effect_matrix() (in module sccoda.util.data_generation) stackbar() (in module sccoda.util.data_visualization) stacked_barplot() (in module sccoda.util.data_visualization) summary() (sccoda.util.result_classes.CAResult method) summary_extended() (sccoda.util.result_classes.CAResult method) summary_prepare() (sccoda.util.result_classes.CAResult method)

T

TTest (class in sccoda.model.other_models)