Index

A

add_figure() (Util.Html method) add_fixed_rank_sortable() (Util.Html method) add_free_content() (Util.Html method) add_heading() (Util.Html method) add_links() (Util.Html method) add_list() (Util.Html method) add_zebra_table() (Util.Html method)

AnnotationSet (class in AnnotationSet) (module) AnnotationSet.DataType (class in AnnotationSet) AnnotationSet.GeneField (class in AnnotationSet) AnnotationSet.ReturnType (class in AnnotationSet) AnnotationSet.TfField (class in AnnotationSet) AuxiliaryFunctions (class in Util)

C

ConfigurationFile (class in Util) correct_standard_bed_score() (Util.AuxiliaryFunctions static method)

create_footer() (Util.Html method) create_header() (Util.Html method)

D

distance() (GenomicRegion.GenomicRegion method)

E

ErrorHandler (class in Util) exact_mapping() (AnnotationSet.AnnotationSet method)

extend() (GenomicRegion.GenomicRegion method) extract_blocks() (GenomicRegion.GenomicRegion method)

F

fix_gene_names() (AnnotationSet.AnnotationSet method)

G

GeneSet (module) GenomeData (class in Util) GenomicRegion (class in GenomicRegion) (module) get() (AnnotationSet.AnnotationSet method) get_annotation_dump_dir() (Util.GenomeData method) get_association_file() (Util.GenomeData method) get_chromosome_sizes() (Util.GenomeData method) get_css_file() (Util.ImageData method) get_data() (GenomicRegion.GenomicRegion method) get_default_bias_table_F() (Util.HmmData method) get_default_bias_table_R() (Util.HmmData method) get_default_hmm_dnase() (Util.HmmData method) get_default_hmm_dnase_bc() (Util.HmmData method) get_default_hmm_dnase_histone() (Util.HmmData method) get_default_hmm_dnase_histone_bc() (Util.HmmData method) get_default_hmm_histone() (Util.HmmData method) get_default_motif_logo() (Util.ImageData method) get_exons() (AnnotationSet.AnnotationSet method) get_fpr_list() (Util.MotifData method) get_gencode_annotation() (Util.GenomeData method) get_gene_alias() (Util.GenomeData method) get_genes() (AnnotationSet.AnnotationSet method)

get_genome() (Util.GenomeData method) get_introns() (AnnotationSet.AnnotationSet method) get_jquery() (Util.ImageData method) get_jquery_metadata() (Util.ImageData method) get_logo_file() (Util.MotifData method) get_logo_list() (Util.MotifData method) get_mtf_list() (Util.MotifData method) get_mtf_path() (Util.MotifData method) get_official_symbol() (AnnotationSet.AnnotationSet method) get_organism() (Util.GenomeData method) get_promoters() (AnnotationSet.AnnotationSet method) get_pwm_list() (Util.MotifData method) get_pwm_path() (Util.MotifData method) get_repositories_list() (Util.MotifData method) get_rgt_logo() (Util.ImageData method) get_sorttable_file() (Util.ImageData method) get_tablesorter() (Util.ImageData method) get_tdf_logo() (Util.ImageData method) get_tss() (AnnotationSet.AnnotationSet method) get_tts() (AnnotationSet.AnnotationSet method) get_viz_logo() (Util.ImageData method)

H

HelpfulOptionParser (class in Util) HmmData (class in Util)

Html (class in Util)

I

ImageData (class in Util)

inexact_mapping() (AnnotationSet.AnnotationSet method)

L

load_alias_dict() (AnnotationSet.AnnotationSet method) load_gene_list() (AnnotationSet.AnnotationSet method)

load_tf_list() (AnnotationSet.AnnotationSet method)

M

map_lists() (AnnotationSet.AnnotationSet method) MotifData (class in Util)

MotifSet (module)

O

overlap() (GenomicRegion.GenomicRegion method) (Util.AuxiliaryFunctions static method)

OverlapType (class in Util)

P

PassThroughOptionParser (class in Util)

S

SequenceType (class in Util) string_is_float() (Util.AuxiliaryFunctions static method)

string_is_int() (Util.AuxiliaryFunctions static method)

T

throw_error() (Util.ErrorHandler method)

throw_warning() (Util.ErrorHandler method)

U

Util (module)

W

write() (Util.Html method)