Index

A

add_experiment() (pytadbit.chromosome.Chromosome method) align() (in module pytadbit.boundary_aligner.aligner) align_experiments() (pytadbit.chromosome.Chromosome method)

Alignment (class in pytadbit.alignment) average_model() (pytadbit.imp.structuralmodels.StructuralModels method)

B

batch_tadbit() (in module pytadbit.tadbit)

C

calc_eqv_rmsd() (in module pytadbit.utils.tadmaths) calinski_harabasz() (in module pytadbit.utils.tadmaths) centroid_model() (pytadbit.imp.structuralmodels.StructuralModels method) Chromosome (class in pytadbit.chromosome)

cluster_analysis_dendrogram() (pytadbit.imp.structuralmodels.StructuralModels method) cluster_models() (pytadbit.imp.structuralmodels.StructuralModels method) contact_map() (pytadbit.imp.structuralmodels.StructuralModels method) correlate_with_real_data() (pytadbit.imp.structuralmodels.StructuralModels method)

D

define_best_models() (pytadbit.imp.structuralmodels.StructuralModels method) density_plot() (pytadbit.imp.structuralmodels.StructuralModels method)

dihedral_angle() (pytadbit.imp.structuralmodels.StructuralModels method) draw() (pytadbit.alignment.Alignment method)

E

Experiment (class in pytadbit.experiment)

ExperimentList (class in pytadbit.chromosome)

F

fetch_model_by_rand_init() (pytadbit.imp.structuralmodels.StructuralModels method)

find_tad() (pytadbit.chromosome.Chromosome method)

G

generate_3d_models() (in module pytadbit.imp.imp_modelling) generate_rnd_tads() (in module pytadbit.alignment) generate_shuffle_tads() (in module pytadbit.alignment) get_column() (pytadbit.alignment.Alignment method) get_contact_matrix() (pytadbit.imp.structuralmodels.StructuralModels method)

get_experiment() (pytadbit.chromosome.Chromosome method) get_hic_matrix() (pytadbit.experiment.Experiment method) get_hic_zscores() (pytadbit.experiment.Experiment method) get_tad_hic() (pytadbit.chromosome.Chromosome method)

H

hic_filtering_for_modelling() (in module pytadbit.utils.hic_filtering)

I

IMPmodel (class in pytadbit.imp.impmodel) IMPoptimizer (class in pytadbit.imp.impoptimizer) iter_tads() (pytadbit.chromosome.Chromosome method)

itercolumns() (pytadbit.alignment.Alignment method) iteritems() (pytadbit.alignment.Alignment method) itervalues() (pytadbit.alignment.Alignment method)

L

load_chromosome() (in module pytadbit.chromosome) load_from_file() (pytadbit.imp.impoptimizer.IMPoptimizer method)

load_hic_data() (pytadbit.experiment.Experiment method) load_tad_def() (pytadbit.experiment.Experiment method)

M

measure_angle_3_particles() (pytadbit.imp.structuralmodels.StructuralModels method) median_3d_dist() (pytadbit.imp.structuralmodels.StructuralModels method)

model_consistency() (pytadbit.imp.structuralmodels.StructuralModels method) model_region() (pytadbit.experiment.Experiment method)

N

needleman_wunsch() (in module pytadbit.boundary_aligner.globally)

normalize_hic() (pytadbit.experiment.Experiment method)

O

objective_function() (pytadbit.imp.impmodel.IMPmodel method) objective_function_model() (pytadbit.imp.structuralmodels.StructuralModels method)

optimal_cmo() (in module pytadbit.tad_clustering.tad_cmo) optimal_imp_parameters() (pytadbit.experiment.Experiment method)

P

parse_tads() (in module pytadbit.parsers.tad_parser) particle_coordinates() (pytadbit.imp.structuralmodels.StructuralModels method) plot_2d() (pytadbit.imp.impoptimizer.IMPoptimizer method) plot_2d_optimization_result() (in module pytadbit.utils.extraviews)

plot_3d() (pytadbit.imp.impoptimizer.IMPoptimizer method) plot_3d_optimization_result() (in module pytadbit.utils.extraviews) print_hic_matrix() (pytadbit.experiment.Experiment method) print_result_r() (in module pytadbit.tadbit)

R

randomization_test() (in module pytadbit.alignment) read_matrix() (in module pytadbit.parsers.hic_parser)

reciprocal() (in module pytadbit.boundary_aligner.reciprocally) run_grid_search() (pytadbit.imp.impoptimizer.IMPoptimizer method)

S

save_chromosome() (pytadbit.chromosome.Chromosome method) save_models() (pytadbit.imp.structuralmodels.StructuralModels method) set_max_tad_size() (pytadbit.chromosome.Chromosome method)

set_resolution() (pytadbit.experiment.Experiment method) smith_waterma() (in module pytadbit.boundary_aligner.locally) StructuralModels (class in pytadbit.imp.structuralmodels)

T

TAD (class in pytadbit.alignment)

tadbit() (in module pytadbit.tadbit)

V

view_model() (pytadbit.imp.impmodel.IMPmodel method) (pytadbit.imp.structuralmodels.StructuralModels method)

visualize() (pytadbit.chromosome.Chromosome method)

W

walking_angle() (pytadbit.imp.structuralmodels.StructuralModels method) walking_dihedral() (pytadbit.imp.structuralmodels.StructuralModels method) write_alignment() (pytadbit.alignment.Alignment method) write_cmm() (pytadbit.imp.impmodel.IMPmodel method) (pytadbit.imp.structuralmodels.StructuralModels method)

write_interaction_pairs() (pytadbit.experiment.Experiment method) write_result() (pytadbit.imp.impoptimizer.IMPoptimizer method) write_xyz() (pytadbit.imp.impmodel.IMPmodel method) (pytadbit.imp.structuralmodels.StructuralModels method)

Z

zscore_plot() (pytadbit.imp.structuralmodels.StructuralModels method)