Index

A

aggregate_signals() (in module metaloci.spatial_stats.lmi)

B

bedparser() (in module metaloci.misc.misc)

binsearcher() (in module metaloci.misc.misc) bts_ratio() (in module metaloci.utility_scripts.bts)

C

check_names() (in module metaloci.misc.misc) clean_matrix() (in module metaloci.misc.misc) compute_lmi() (in module metaloci.spatial_stats.lmi)

construct_voronoi() (in module metaloci.spatial_stats.lmi) create_composite_figure() (in module metaloci.plot.plot) create_number_image() (in module metaloci.plot.plot) create_version_log() (in module metaloci.misc.misc)

E

estimate_cutoff() (in module metaloci.graph_layout.kk)

estimate_persistence_length() (in module metaloci.graph_layout.kk)

G

get_bed() (in module metaloci.spatial_stats.lmi) get_figures() (in module metaloci.tools.figure) get_gaudi_signal_plot() (in module metaloci.plot.plot) get_gaudi_type_plot() (in module metaloci.plot.plot) get_hic_plot() (in module metaloci.plot.plot) get_highlight() (in module metaloci.plot.plot) get_kk_plot() (in module metaloci.plot.plot)

get_lmi() (in module metaloci.tools.ml) get_lmi_change_scan_plot() (in module metaloci.plot.plot) get_lmi_scatterplot() (in module metaloci.plot.plot) get_poi_data() (in module metaloci.misc.misc) get_region_layout() (in module metaloci.tools.layout) get_restraints_matrix() (in module metaloci.graph_layout.kk) get_subset_matrix() (in module metaloci.graph_layout.kk) gtfparser() (in module metaloci.misc.misc)

H

has_exactly_one_line() (in module metaloci.misc.misc)

K

kk_plot_to_subplot() (in module metaloci.plot.plot)

L

load_region_signals() (in module metaloci.spatial_stats.lmi)

M

metaloci module metaloci.graph_layout module metaloci.graph_layout.kk module metaloci.misc module metaloci.misc.misc module metaloci.mlo module metaloci.plot module metaloci.plot.plot module metaloci.spatial_stats module metaloci.spatial_stats.lmi module metaloci.tests module metaloci.tests.test_tools module metaloci.tools module metaloci.tools.figure module metaloci.tools.layout module metaloci.tools.ml module metaloci.tools.prep module

metaloci.utility_scripts module metaloci.utility_scripts.bts module metaloci.utility_scripts.gene_selector module metaloci.utility_scripts.sniffer module MetalociObject (class in metaloci.mlo) mixed_matrices_plot() (in module metaloci.plot.plot) module metaloci metaloci.graph_layout metaloci.graph_layout.kk metaloci.misc metaloci.misc.misc metaloci.mlo metaloci.plot metaloci.plot.plot metaloci.spatial_stats metaloci.spatial_stats.lmi metaloci.tests metaloci.tests.test_tools metaloci.tools metaloci.tools.figure metaloci.tools.layout metaloci.tools.ml metaloci.tools.prep metaloci.utility_scripts metaloci.utility_scripts.bts metaloci.utility_scripts.gene_selector metaloci.utility_scripts.sniffer

P

param_search() (in module metaloci.utility_scripts.bts) pl_estimation() (in module metaloci.utility_scripts.bts)

place_composite() (in module metaloci.plot.plot) place_pdf() (in module metaloci.plot.plot)

R

reconstruct() (in module metaloci.mlo) run() (in module metaloci.tools.figure) (in module metaloci.tools.layout) (in module metaloci.tools.ml) (in module metaloci.tools.prep) (in module metaloci.utility_scripts.bts) (in module metaloci.utility_scripts.gene_selector) (in module metaloci.utility_scripts.sniffer)

S

save() (metaloci.mlo.MetalociObject method) save_mm_kk() (in module metaloci.plot.plot) signal_binnarize() (in module metaloci.misc.misc)

signal_normalization() (in module metaloci.misc.misc) signal_plot() (in module metaloci.plot.plot) sum_hic_columns() (in module metaloci.utility_scripts.bts)

U

ucscparser() (in module metaloci.misc.misc)

W

write_bad_region() (in module metaloci.misc.misc)

write_bed() (in module metaloci.misc.misc) write_moran_data() (in module metaloci.misc.misc)