Index

A

add_coord_frequency_table() (in module snaf.snaf) add_gene_symbol_frequency_table() (in module snaf.downstream)

add_tumor_specificity_frequency_table() (in module snaf.gtex) analyze_neoantigens() (in module snaf.downstream)

C

calculate_psi() (in module snaf.downstream)

chop_normal_pep_db() (in module snaf.proteomics) compare_two_fasta() (in module snaf.proteomics)

E

enhance_frequency_table() (in module snaf.snaf)

G

generate_full_results() (in module snaf.surface.main) generate_results() (in module snaf.surface.main) (snaf.snaf.JunctionCountMatrixQuery static method) get_all_normal_h5ad() (in module snaf.gtex) get_coverage() (in module snaf.downstream) get_membrane_tuples() (snaf.snaf.JunctionCountMatrixQuery static method)

gtex_visual_combine() (in module snaf.gtex_viewer) gtex_visual_combine_barplot() (in module snaf.gtex_viewer) gtex_visual_combine_plotly() (in module snaf.gtex_viewer) gtex_visual_norm_count_combined() (in module snaf.gtex_viewer) gtex_visual_per_tissue_count() (in module snaf.gtex_viewer) gtex_visual_subplots() (in module snaf.gtex_viewer)

I

initialize() (in module snaf.__init__) (in module snaf.surface.main)

J

JunctionCountMatrixQuery (class in snaf.snaf)

M

mutation_analysis() (in module snaf.downstream)

P

plot_event_type() (in module snaf.downstream) prepare_DEG_analysis() (in module snaf.downstream)

prepare_GO_analysis() (in module snaf.downstream) prepare_sashimi_plot() (in module snaf.downstream)

R

remove_redundant() (in module snaf.proteomics) report_candidates() (in module snaf.downstream) (in module snaf.surface.main)

run() (in module snaf.surface.main) (snaf.snaf.JunctionCountMatrixQuery method) run_dash_B_antigen() (in module snaf.surface.main) run_dash_T_antigen() (in module snaf.dash_app.app)

S

set_maxquant_configuration() (in module snaf.proteomics) show_neoantigen_as_fasta() (snaf.snaf.JunctionCountMatrixQuery method)

summarize_ms_result() (in module snaf.proteomics) survival_analysis() (in module snaf.downstream) survival_regression() (in module snaf.downstream)

V

visualize() (snaf.snaf.JunctionCountMatrixQuery method)

visualize_DEG_result() (in module snaf.downstream) visualize_GO_result() (in module snaf.downstream)