Index

A

accessibility() (pytadbit.modelling.structuralmodels.StructuralModels method) add_experiment() (pytadbit.chromosome.Chromosome method) add_sections() (pytadbit.hic_data.HiC_data method) add_sections_from_fasta() (pytadbit.hic_data.HiC_data method) align() (in module pytadbit.boundary_aligner.aligner) align_experiments() (pytadbit.chromosome.Chromosome method)

align_models() (pytadbit.modelling.structuralmodels.StructuralModels method) Alignment (class in pytadbit.alignment) angle_between_3_particles() (pytadbit.modelling.structuralmodels.StructuralModels method) angle_between_3_points() (in module pytadbit.utils.three_dim_stats) append() (pytadbit.chromosome.ExperimentList method) apply_filter() (in module pytadbit.mapping.filter) average_model() (pytadbit.modelling.structuralmodels.StructuralModels method)

B

batch_tadbit() (in module pytadbit.tadbit)

C

calc_eqv_rmsd() (in module pytadbit.utils.three_dim_stats) calinski_harabasz() (in module pytadbit.utils.tadmaths) centroid_model() (pytadbit.modelling.structuralmodels.StructuralModels method) chimera_view() (in module pytadbit.utils.extraviews) Chromosome (class in pytadbit.chromosome) cis_trans_ratio() (pytadbit.hic_data.HiC_data method)

cluster_analysis_dendrogram() (pytadbit.modelling.structuralmodels.StructuralModels method) cluster_models() (pytadbit.modelling.structuralmodels.StructuralModels method) color_residues() (in module pytadbit.utils.extraviews) compare_models() (in module pytadbit.utils.extraviews) contact_map() (pytadbit.modelling.structuralmodels.StructuralModels method) correlate_matrices() (in module pytadbit.mapping.analyze) correlate_with_real_data() (pytadbit.modelling.structuralmodels.StructuralModels method)

D

deconvolve() (pytadbit.modelling.structuralmodels.StructuralModels method) define_best_models() (pytadbit.modelling.structuralmodels.StructuralModels method) density_plot() (pytadbit.modelling.structuralmodels.StructuralModels method)

dihedral() (in module pytadbit.utils.three_dim_stats) dihedral_angle() (pytadbit.modelling.structuralmodels.StructuralModels method) distance() (in module pytadbit.utils.three_dim_stats) draw() (pytadbit.alignment.Alignment method)

E

eig_correlate_matrices() (in module pytadbit.mapping.analyze)

Experiment (class in pytadbit.experiment) ExperimentList (class in pytadbit.chromosome)

F

fetch_model_by_rand_init() (pytadbit.modelling.structuralmodels.StructuralModels method) filter_columns() (pytadbit.experiment.Experiment method) (pytadbit.hic_data.HiC_data method) filter_reads() (in module pytadbit.mapping.filter)

find_compartments() (pytadbit.hic_data.HiC_data method) find_compartments_beta() (pytadbit.hic_data.HiC_data method) find_tad() (pytadbit.chromosome.Chromosome method) full_mapping() (in module pytadbit.mapping.full_mapper)

G

generate_circle_points() (in module pytadbit.utils.three_dim_stats) generate_rnd_tads() (in module pytadbit.alignment) generate_shuffle_tads() (in module pytadbit.alignment) get_column() (pytadbit.alignment.Alignment method) get_contact_matrix() (pytadbit.modelling.structuralmodels.StructuralModels method) get_dependencies_version() (in module pytadbit) get_experiment() (pytadbit.chromosome.Chromosome method)

get_free_space_mb() (in module pytadbit.utils.file_handling) get_hic_data_as_csr() (pytadbit.hic_data.HiC_data method) get_hic_matrix() (pytadbit.experiment.Experiment method) get_hic_zscores() (pytadbit.experiment.Experiment method) get_intersection() (in module pytadbit.mapping) get_matrix() (pytadbit.hic_data.HiC_data method) get_persistence_length() (pytadbit.modelling.structuralmodels.StructuralModels method) get_tad_hic() (pytadbit.chromosome.Chromosome method)

H

HiC_data (class in pytadbit.hic_data)

hic_filtering_for_modelling() (in module pytadbit.utils.hic_filtering) hic_map() (in module pytadbit.mapping.analyze)

I

IMPmodel (class in pytadbit.modelling.impmodel) infer_unrestrained_particle_coords() (pytadbit.modelling.structuralmodels.StructuralModels method) insert_sizes() (in module pytadbit.mapping.analyze) interactions() (pytadbit.modelling.structuralmodels.StructuralModels method)

iter_tads() (pytadbit.chromosome.Chromosome method) itercolumns() (pytadbit.alignment.Alignment method) iteritems() (pytadbit.alignment.Alignment method) itervalues() (pytadbit.alignment.Alignment method)

L

load_biases() (pytadbit.hic_data.HiC_data method) load_chromosome() (in module pytadbit.chromosome) load_experiment_from_reads() (in module pytadbit.experiment) load_hic_data() (pytadbit.experiment.Experiment method) load_hic_data_from_reads() (in module pytadbit.parsers.hic_parser)

load_impmodel_from_cmm() (in module pytadbit.modelling.impmodel) load_impmodel_from_xyz() (in module pytadbit.modelling.impmodel) load_norm_data() (pytadbit.experiment.Experiment method) load_structuralmodels() (in module pytadbit.modelling.structuralmodels) load_tad_def() (pytadbit.experiment.Experiment method)

M

magic_open() (in module pytadbit.utils.file_handling) map_re_sites() (in module pytadbit.mapping.restriction_enzymes) median_3d_dist() (pytadbit.modelling.structuralmodels.StructuralModels method)

merge_2d_beds() (in module pytadbit.mapping) model_consistency() (pytadbit.modelling.structuralmodels.StructuralModels method) model_region() (pytadbit.experiment.Experiment method)

N

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

normalize_hic() (pytadbit.experiment.Experiment method) (pytadbit.hic_data.HiC_data method)

O

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

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

P

parse_fasta() (in module pytadbit.parsers.genome_parser) parse_sam() (in module pytadbit.parsers.sam_parser) parse_tads() (in module pytadbit.parsers.tad_parser) particle_coordinates() (pytadbit.modelling.structuralmodels.StructuralModels method) plot_2d_optimization_result() (in module pytadbit.utils.extraviews) plot_3d_model() (in module pytadbit.utils.extraviews)

plot_3d_optimization_result() (in module pytadbit.utils.extraviews) plot_distance_vs_interactions() (in module pytadbit.mapping.analyze) plot_genomic_distribution() (in module pytadbit.mapping.analyze) plot_iterative_mapping() (in module pytadbit.mapping.analyze) plot_strand_bias_by_distance() (in module pytadbit.mapping.analyze) print_hic_matrix() (pytadbit.experiment.Experiment method) print_result_r() (in module pytadbit.tadbit)

Q

quality_plot() (in module pytadbit.utils.fastq_utils)

R

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

reciprocal() (in module pytadbit.boundary_aligner.reciprocally) repaired() (in module pytadbit.mapping.restriction_enzymes)

S

save_biases() (pytadbit.hic_data.HiC_data method) save_chromosome() (pytadbit.chromosome.Chromosome method) save_models() (pytadbit.modelling.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) square_distance() (in module pytadbit.utils.three_dim_stats) StructuralModels (class in pytadbit.modelling.structuralmodels) sum() (pytadbit.hic_data.HiC_data method)

T

TAD (class in pytadbit.alignment) tad_border_coloring() (in module pytadbit.utils.extraviews)

tad_coloring() (in module pytadbit.utils.extraviews) tad_density_plot() (pytadbit.chromosome.Chromosome method) tadbit() (in module pytadbit.tadbit)

V

view() (pytadbit.experiment.Experiment method) view_centroid() (pytadbit.modelling.structuralmodels.StructuralModels method)

view_models() (pytadbit.modelling.structuralmodels.StructuralModels method) visualize() (pytadbit.chromosome.Chromosome method)

W

walking_angle() (pytadbit.modelling.structuralmodels.StructuralModels method) walking_dihedral() (pytadbit.modelling.structuralmodels.StructuralModels method) write_alignment() (pytadbit.alignment.Alignment method) write_cmm() (pytadbit.modelling.structuralmodels.StructuralModels method) write_compartments() (pytadbit.hic_data.HiC_data method) write_cooler() (pytadbit.hic_data.HiC_data method) write_coord_table() (pytadbit.hic_data.HiC_data method)

write_interaction_pairs() (pytadbit.experiment.Experiment method) write_json() (pytadbit.experiment.Experiment method) (pytadbit.modelling.structuralmodels.StructuralModels method) write_matrix() (pytadbit.hic_data.HiC_data method) write_tad_borders() (pytadbit.experiment.Experiment method) write_xyz() (pytadbit.modelling.structuralmodels.StructuralModels method) write_xyz_babel() (pytadbit.modelling.structuralmodels.StructuralModels method)

Y

yield_matrix() (pytadbit.hic_data.HiC_data method)

Z

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