Index

A

adjecent_grn_score() (in module splicejac.plot) (in module splicejac.plot.grn_comparison)

B

bif_GRN() (in module splicejac.plot) (in module splicejac.plot.grn_plots)

C

circle_pos() (in module splicejac.plot.grn_plots) coeff_dist() (in module splicejac.tools.regr_method_sens) compare_scvelo_scores() (in module splicejac.plot) (in module splicejac.plot.instability) compare_standout_genes() (in module splicejac.plot) (in module splicejac.plot.gene_variation) compare_wrong_signs() (in module splicejac.plot.plotting_util) compute_avg_jac() (in module splicejac.tools.estimate_jacobian) compute_metrics() (in module splicejac.tools.grn_statistics)

conserved_grn() (in module splicejac.plot) (in module splicejac.plot.grn_plots) construct_jac() (in module splicejac.tools.aux_functions) core_GRN() (in module splicejac.plot) (in module splicejac.plot.grn_plots) count_pos_eig() (in module splicejac.plot.plotting_util) count_sign_change() (in module splicejac.tools.subsampling_sens) count_weight_sign() (in module splicejac.tools.subsampling_sens) count_wrong_signs() (in module splicejac.plot.plotting_util)

D

diff_interactions() (in module splicejac.plot) (in module splicejac.plot.grn_plots)

diff_network() (in module splicejac.plot) (in module splicejac.plot.grn_plots)

E

edge_detection_score() (in module splicejac.tools.grn_comparison) eigen_spectrum() (in module splicejac.plot) (in module splicejac.plot.jacobian_visual) estimate_degr() (in module splicejac.tools.aux_functions) estimate_jacobian() (in module splicejac.tools) (in module splicejac.tools.estimate_jacobian)

export_grn() (in module splicejac.tools) (in module splicejac.tools.export_methods) export_transition_scores() (in module splicejac.tools) (in module splicejac.tools.export_methods)

F

find_dir() (in module splicejac.tools.transitions)

find_trans_genes() (in module splicejac.tools.transitions)

G

gene_var_detail() (in module splicejac.plot) (in module splicejac.plot.gene_variation) gene_var_scatter() (in module splicejac.plot) (in module splicejac.plot.gene_variation) gene_variation() (in module splicejac.plot) (in module splicejac.plot.gene_variation)

GRN_cluster_variation() (in module splicejac.tools.grn_statistics) grn_comparison() (in module splicejac.tools) (in module splicejac.tools.grn_comparison) grn_statistics() (in module splicejac.tools) (in module splicejac.tools.grn_statistics) grn_to_csv() (in module splicejac.tools.export_methods)

I

initial_check() (in module splicejac.tools.estimate_jacobian)

instability_scores() (in module splicejac.tools.aux_functions)

J

jac_regr_cons() (in module splicejac.plot.plotting_util)

L

long_regression() (in module splicejac.tools.estimate_jacobian)

M

mat_distance() (in module splicejac.tools.subsampling_sens) module splicejac splicejac.pl splicejac.plot splicejac.plot.gene_variation splicejac.plot.grn_comparison splicejac.plot.grn_plots splicejac.plot.instability splicejac.plot.jacobian_visual splicejac.plot.plotting_util splicejac.plot.sankey_plots splicejac.plot.sensitivity splicejac.plot.signaling splicejac.plot.umap_scatter splicejac.tl splicejac.tools splicejac.tools.aux_functions splicejac.tools.estimate_jacobian splicejac.tools.export_methods splicejac.tools.grn_comparison splicejac.tools.grn_statistics splicejac.tools.regr_method_sens splicejac.tools.subsampling_sens splicejac.tools.transitions

N

NormalizeData() (in module splicejac.plot.grn_plots)

P

parameter_regression() (in module splicejac.tools.aux_functions) plot_grn() (in module splicejac.plot.grn_plots) plot_grn_comparison() (in module splicejac.plot) (in module splicejac.plot.grn_comparison) plot_setup() (in module splicejac.plot) (in module splicejac.plot.plotting_util)

plot_signaling_change() (in module splicejac.plot) (in module splicejac.plot.signaling) plot_signaling_hubs() (in module splicejac.plot) (in module splicejac.plot.signaling) plot_trans_genes() (in module splicejac.plot) (in module splicejac.plot.instability)

Q

quick_regression() (in module splicejac.tools.estimate_jacobian)

R

regr_method_sens() (in module splicejac.tools) (in module splicejac.tools.regr_method_sens) regression_sens() (in module splicejac.plot) (in module splicejac.plot.sensitivity)

rescale_counts() (in module splicejac.tools.estimate_jacobian) robust_mean() (in module splicejac.plot.grn_plots)

S

sampling_sens() (in module splicejac.plot) (in module splicejac.plot.sensitivity) scatter_scores() (in module splicejac.plot) (in module splicejac.plot.instability) select_top_trans_genes() (in module splicejac.tools.transitions) set_gene_axes() (in module splicejac.tools.aux_functions) set_plot_name() (in module splicejac.plot.gene_variation) sign_detection_score() (in module splicejac.tools.grn_comparison) signaling_score() (in module splicejac.tools.grn_statistics) spectrum_plot() (in module splicejac.plot.jacobian_visual) splicejac module splicejac.pl module splicejac.plot module splicejac.plot.gene_variation module splicejac.plot.grn_comparison module splicejac.plot.grn_plots module splicejac.plot.instability module splicejac.plot.jacobian_visual module splicejac.plot.plotting_util module splicejac.plot.sankey_plots module

splicejac.plot.sensitivity module splicejac.plot.signaling module splicejac.plot.umap_scatter module splicejac.tl module splicejac.tools module splicejac.tools.aux_functions module splicejac.tools.estimate_jacobian module splicejac.tools.export_methods module splicejac.tools.grn_comparison module splicejac.tools.grn_statistics module splicejac.tools.regr_method_sens module splicejac.tools.subsampling_sens module splicejac.tools.transitions module subsample_stability() (in module splicejac.plot) (in module splicejac.plot.sensitivity) subsampling_sens() (in module splicejac.tools) (in module splicejac.tools.subsampling_sens) subset_jacobian() (in module splicejac.plot.grn_plots)

T

test_sub_sampling() (in module splicejac.tools.subsampling_sens) tg_bif_sankey() (in module splicejac.plot) (in module splicejac.plot.sankey_plots) top_conserved_int() (in module splicejac.plot) (in module splicejac.plot.grn_plots)

trans_from_PAGA() (in module splicejac.tools) (in module splicejac.tools.transitions) transition_genes() (in module splicejac.tools) (in module splicejac.tools.transitions)

U

umap_scatter() (in module splicejac.plot) (in module splicejac.plot.umap_scatter)

V

visualize_jacobian() (in module splicejac.plot) (in module splicejac.plot.jacobian_visual)

visualize_network() (in module splicejac.plot) (in module splicejac.plot.grn_plots)