Index

_

__dict__ (xclone.BAF_General_config attribute) (xclone.Combine_General_config attribute) (xclone.HMM_Configs attribute) (xclone.PreprocessingConfig attribute) (xclone.RDR_General_config attribute) (xclone.Smartseq_Config attribute) (xclone.Spatial_Config attribute) (xclone.XCloneConfig attribute) (xclone.XCloneGeneral_config attribute) __init__() (xclone.BAF_General_config method) (xclone.Combine_General_config method) (xclone.HMM_Configs method) (xclone.PreprocessingConfig method) (xclone.RDR_General_config method) (xclone.Smartseq_Config method) (xclone.Spatial_Config method) (xclone.XCloneConfig method) (xclone.XCloneGeneral_config method) __module__ (xclone.BAF_General_config attribute) (xclone.Combine_General_config attribute) (xclone.HMM_Configs attribute) (xclone.PreprocessingConfig attribute) (xclone.RDR_General_config attribute) (xclone.Smartseq_Config attribute) (xclone.Spatial_Config attribute) (xclone.XCloneConfig attribute) (xclone.XCloneGeneral_config attribute)

__str__() (xclone.XCloneConfig method) __weakref__ (xclone.BAF_General_config attribute) (xclone.Combine_General_config attribute) (xclone.HMM_Configs attribute) (xclone.PreprocessingConfig attribute) (xclone.RDR_General_config attribute) (xclone.Smartseq_Config attribute) (xclone.Spatial_Config attribute) (xclone.XCloneConfig attribute) (xclone.XCloneGeneral_config attribute) _Format (xclone.XCloneConfig attribute) _frameon (xclone.XCloneConfig attribute) _is_run_from_ipython() (xclone.XCloneConfig static method) _start (xclone.XCloneConfig attribute) _vector_friendly (xclone.XCloneConfig attribute)

A

AD_file (xclone.PreprocessingConfig attribute)

anno_file_sep (xclone.PreprocessingConfig attribute)

B

BAF_adata_file (xclone.PreprocessingConfig attribute) BAF_add (xclone.BAF_General_config attribute) baf_bias_mode (xclone.BAF_General_config attribute) BAF_CNV_visualization() (in module xclone.plot) baf_data_dir (xclone.PreprocessingConfig attribute) BAF_denoise (xclone.BAF_General_config attribute) (xclone.Combine_General_config attribute)

BAF_denoise_cellprop_cutoff (xclone.BAF_General_config attribute) BAF_denoise_GMM_comp (xclone.BAF_General_config attribute) BAF_denoise_GMM_detection (xclone.BAF_General_config attribute) BAF_General_config (class in xclone) barcodes_key (xclone.PreprocessingConfig attribute) bin_nproc (xclone.BAF_General_config attribute)

C

cell_anno_file (xclone.PreprocessingConfig attribute) cell_anno_key (xclone.PreprocessingConfig attribute) (xclone.XCloneGeneral_config attribute) CNV_N_components (xclone.BAF_General_config attribute) (xclone.HMM_Configs attribute) CNV_visualization() (in module xclone.plot) Combine_CNV_visualization() (in module xclone.plot) Combine_General_config (class in xclone) Complex_BAF_CNV_visualization() (in module xclone.plot) Complex_CNV_visualization() (in module xclone.plot)

Complex_Combine_CNV_visualization() (in module xclone.plot) concentration (xclone.BAF_General_config attribute) (xclone.Smartseq_Config attribute) (xclone.Spatial_Config attribute) concentration_lower (xclone.BAF_General_config attribute) concentration_upper (xclone.BAF_General_config attribute) copygain_correct (xclone.Combine_General_config attribute) copygain_correct_mode (xclone.Combine_General_config attribute) copyloss_correct (xclone.Combine_General_config attribute) copyloss_correct_mode (xclone.Combine_General_config attribute) customizedplotting (xclone.Combine_General_config attribute)

D

dataset_name (xclone.PreprocessingConfig attribute) develop_mode (xclone.XCloneGeneral_config attribute) dispersion_celltype (xclone.RDR_General_config attribute)

display() (xclone.PreprocessingConfig method) (xclone.XCloneConfig method) DP_file (xclone.PreprocessingConfig attribute)

E

exclude_XY (xclone.Smartseq_Config attribute) (xclone.Spatial_Config attribute) (xclone.XCloneGeneral_config attribute)

extra_anno() (in module xclone.preprocessing) extreme_count_cap (xclone.BAF_General_config attribute) (xclone.Smartseq_Config attribute) (xclone.Spatial_Config attribute)

F

feature_mode (xclone.BAF_General_config attribute) file_format_data (xclone.XCloneConfig property) file_format_figs (xclone.XCloneConfig property)

filter_ref_ave (xclone.RDR_General_config attribute) (xclone.Smartseq_Config attribute) (xclone.Spatial_Config attribute) fit_GLM_libratio (xclone.RDR_General_config attribute)

G

gene_exp_group (xclone.RDR_General_config attribute) gene_exp_ref_log (xclone.RDR_General_config attribute) gene_specific_concentration (xclone.BAF_General_config attribute) (xclone.Smartseq_Config attribute) (xclone.Spatial_Config attribute) genome_mode (xclone.PreprocessingConfig attribute)

get_BAF_KNN_connectivities (xclone.BAF_General_config attribute) get_marker_genes (xclone.RDR_General_config attribute) guide_chr_anno_key (xclone.RDR_General_config attribute) guide_cnv_ratio (xclone.RDR_General_config attribute) guide_qt_lst (xclone.RDR_General_config attribute) guide_theo_CNV_states (xclone.BAF_General_config attribute)

H

HMM_brk (xclone.HMM_Configs attribute)

HMM_Configs (class in xclone)

K

KNN_connect_use_key (xclone.BAF_General_config attribute)

KNN_neighbors (xclone.XCloneGeneral_config attribute) KNN_Xlayer (xclone.BAF_General_config attribute)

L

Literal (xclone.XCloneConfig attribute)

M

marker_group_anno_key (xclone.RDR_General_config attribute) max_iter (xclone.HMM_Configs attribute) merge_loh (xclone.Combine_General_config attribute) merge_loss (xclone.Combine_General_config attribute) min_gene_keep_num (xclone.RDR_General_config attribute) (xclone.Spatial_Config attribute) min_iter (xclone.HMM_Configs attribute)

module xclone module (xclone.HMM_Configs attribute) (xclone.PreprocessingConfig attribute) (xclone.Smartseq_Config attribute) (xclone.Spatial_Config attribute) mtx_barcodes_file (xclone.PreprocessingConfig attribute) multi_refcelltype (xclone.RDR_General_config attribute)

O

outdir (xclone.XCloneConfig property)

P

phasing_len (xclone.BAF_General_config attribute) phasing_region_key (xclone.BAF_General_config attribute) plot_cell_anno_key (xclone.BAF_General_config attribute) (xclone.Combine_General_config attribute) (xclone.RDR_General_config attribute)

plot_immune_celltype (xclone.XCloneGeneral_config attribute) plot_ref_celltype (xclone.XCloneGeneral_config attribute) plot_remove_immune (xclone.XCloneGeneral_config attribute) plot_remove_reference (xclone.XCloneGeneral_config attribute) plot_suffix (xclone.XCloneConfig property) PreprocessingConfig (class in xclone)

R

RDR_adata_file (xclone.PreprocessingConfig attribute) rdr_data_dir (xclone.PreprocessingConfig attribute) RDR_denoise (xclone.Combine_General_config attribute) RDR_file (xclone.BAF_General_config attribute) (xclone.PreprocessingConfig attribute) RDR_General_config (class in xclone) rdr_plot_vmax (xclone.RDR_General_config attribute) rdr_plot_vmin (xclone.RDR_General_config attribute) RDR_prior (xclone.Combine_General_config attribute) readrdr_mtx() (in module xclone.preprocessing)

ref_BAF_clip (xclone.BAF_General_config attribute) ref_celltype (xclone.XCloneGeneral_config attribute) regions_anno_file (xclone.PreprocessingConfig attribute) remove_guide_XY (xclone.Smartseq_Config attribute) (xclone.Spatial_Config attribute) (xclone.XCloneGeneral_config attribute) remove_marker (xclone.RDR_General_config attribute) remove_marker_genes (xclone.BAF_General_config attribute) run_BAF() (in module xclone.model) run_combine() (in module xclone.model) run_RDR() (in module xclone.model)

S

select_normal_chr_num (xclone.RDR_General_config attribute) set_figtitle (xclone.BAF_General_config attribute) (xclone.Combine_General_config attribute) (xclone.RDR_General_config attribute) set_figure_params() (xclone.XCloneConfig method) set_spatial (xclone.PreprocessingConfig attribute) smart_transform (xclone.RDR_General_config attribute) (xclone.Smartseq_Config attribute) (xclone.Spatial_Config attribute)

Smartseq_Config (class in xclone) Spatial_Config (class in xclone) spatial_transform (xclone.Spatial_Config attribute) spot_position_file (xclone.PreprocessingConfig attribute) start_prob (xclone.HMM_Configs attribute) (xclone.Smartseq_Config attribute) (xclone.Spatial_Config attribute)

T

theo_neutral_BAF (xclone.BAF_General_config attribute) top_n_marker (xclone.RDR_General_config attribute)

trans_prob (xclone.HMM_Configs attribute) trans_t (xclone.HMM_Configs attribute)

U

update_info_from_rdr (xclone.BAF_General_config attribute)

V

visualize_cell_BAF() (in module xclone.plot)

W

WGD_cell_prop_threshold (xclone.Combine_General_config attribute) WGD_detect_genome_level (xclone.Combine_General_config attribute) WGD_detection (xclone.Combine_General_config attribute) WGD_prop_value_threshold (xclone.Combine_General_config attribute) WMA_smooth_key (xclone.BAF_General_config attribute) (xclone.RDR_General_config attribute)

WMA_window_size (xclone.BAF_General_config attribute) (xclone.RDR_General_config attribute) (xclone.Smartseq_Config attribute) (xclone.Spatial_Config attribute)

X

xclone module xclone_plot (xclone.BAF_General_config attribute) (xclone.Combine_General_config attribute) (xclone.RDR_General_config attribute)

XCloneConfig (class in xclone) xclonedata() (in module xclone.preprocessing) XCloneGeneral_config (class in xclone)