Index

Symbols

-a scenic_pipeline.sh command line option -o scenic_pipeline.sh command line option

-s scenic_pipeline.sh command line option

_

__init__() (cell_pipeline.CellPipeline method) (grn_pipeline.GRNPipeline method) (sample_pipeline.SamplePipeline method)

C

calc_distance() (cell_pipeline.CellPipeline method) calc_distance_point() (cell_pipeline.CellPipeline method)

CellPipeline (class in cell_pipeline) classify_exp_level() (cell_pipeline.CellPipeline method) clean_data() (cell_pipeline.CellPipeline method)

D

detect_outliers() (cell_pipeline.CellPipeline method)

dotplot() (cell_pipeline.CellPipeline method)

E

explain_expr_celltypes() (cell_pipeline.CellPipeline method)

expression_vs_detection() (cell_pipeline.CellPipeline method)

F

find_TFs() (grn_pipeline.GRNPipeline method) find_thresholds() (cell_pipeline.CellPipeline method)

fit_spline() (cell_pipeline.CellPipeline method) format_gene_summary() (grn_pipeline.GRNPipeline method)

G

genegene_importance_histograms() (grn_pipeline.GRNPipeline method) get_adata() (cell_pipeline.CellPipeline method) get_entrez_gene_summary() (grn_pipeline.GRNPipeline method) get_gene_summary() (grn_pipeline.GRNPipeline method) get_genesets() (grn_pipeline.GRNPipeline method) get_goi_pathways() (grn_pipeline.GRNPipeline method) get_reactome() (grn_pipeline.GRNPipeline method)

get_regulon_genes() (grn_pipeline.GRNPipeline method) get_regulon_geneset() (grn_pipeline.GRNPipeline method) get_regulon_genesets() (grn_pipeline.GRNPipeline method) gGOSt() (grn_pipeline.GRNPipeline method) gGOSt_listed() (grn_pipeline.GRNPipeline method) gmt_to_decoupler() (grn_pipeline.GRNPipeline static method) GOI_network_stats() (grn_pipeline.GRNPipeline method) GRNPipeline (class in grn_pipeline)

H

heatmap() (cell_pipeline.CellPipeline method)

L

list_outliers() (cell_pipeline.CellPipeline method)

M

make_adj_df() (grn_pipeline.GRNPipeline method) make_df() (cell_pipeline.CellPipeline method) make_gene_gene_network() (grn_pipeline.GRNPipeline method)

make_goi_grn() (grn_pipeline.GRNPipeline method) make_network() (grn_pipeline.GRNPipeline method) make_regulon_dataframe() (grn_pipeline.GRNPipeline method) matrixplot() (cell_pipeline.CellPipeline method)

P

pl_sample_celltype() (sample_pipeline.SamplePipeline method) pl_violin() (sample_pipeline.SamplePipeline method) plot_expr_class() (cell_pipeline.CellPipeline method) plot_expressions() (cell_pipeline.CellPipeline method)

plot_outliers() (cell_pipeline.CellPipeline method) plot_pathways() (grn_pipeline.GRNPipeline method) plot_regulon_expression() (grn_pipeline.GRNPipeline method) plot_umap() (cell_pipeline.CellPipeline method)

S

sample_v_celltype() (sample_pipeline.SamplePipeline method) SamplePipeline (class in sample_pipeline) scenic_pipeline.sh command line option -a -o -s

show_network() (grn_pipeline.GRNPipeline method)