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A
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C
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D
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E
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F
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G
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H
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I
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L
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M
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O
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P
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S
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T
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U
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W
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)
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