Index

A

align_with_gene_list() (deside.utility.read_file.ReadExp method)

B

BulkGEPGenerator (class in deside.simulation)

D

DeSide (class in deside.decon_cf) deside.bulk_cell module deside.decon_cf module deside.plot module

deside.simulation module deside.utility module do_scaling() (deside.utility.read_file.ReadExp method) do_scaling_by_constant() (deside.utility.read_file.ReadExp method)

F

filtering_by_gene_list_and_pca_plot() (in module deside.simulation)

G

generate_frac_sc() (deside.simulation.SingleCellTypeGEPGenerator method) generate_gep() (deside.simulation.BulkGEPGenerator method) generate_samples() (deside.simulation.SingleCellTypeGEPGenerator method) get_cell_fraction() (deside.utility.read_file.ReadH5AD method) get_df() (deside.utility.read_file.ReadH5AD method) get_exp() (deside.utility.read_file.ReadExp method)

get_file_type() (deside.utility.read_file.ReadExp method) get_gene_list_for_filtering() (in module deside.simulation) get_h5ad() (deside.utility.read_file.ReadH5AD method) get_model() (deside.decon_cf.DeSide method) get_parameters() (deside.decon_cf.DeSide method) get_x_before_predict() (deside.decon_cf.DeSide method)

L

log_exp2cpm() (in module deside.utility)

M

module deside.bulk_cell deside.decon_cf deside.plot deside.simulation deside.utility

N

non_log2cpm() (in module deside.utility)

non_log2log_cpm() (in module deside.utility)

P

plot_corr_two_columns() (in module deside.plot)

plot_predicted_result() (in module deside.plot) predict() (deside.decon_cf.DeSide method)

R

random_generation_fraction() (in module deside.simulation) read_counts2tpm() (in module deside.bulk_cell)

read_data_from_h5ad() (in module deside.utility) ReadExp (class in deside.utility.read_file) ReadH5AD (class in deside.utility.read_file)

S

save() (deside.utility.read_file.ReadExp method)

segment_generation_fraction() (in module deside.simulation) SingleCellTypeGEPGenerator (class in deside.simulation)

T

to_log2cpm1p() (deside.utility.read_file.ReadExp method)

to_tpm() (deside.utility.read_file.ReadExp method) train_model() (deside.decon_cf.DeSide method)