Index

A

add() (CoverageSet.CoverageSet method) (GenomicRegionSet.GenomicRegionSet method) (MotifSet.MotifSet method) 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) any_chrom() (GenomicRegionSet.GenomicRegionSet method) AuxiliaryFunctions (class in Util)

B

by_names() (GenomicRegionSet.GenomicRegionSet method)

C

change_name_by_dict() (GenomicRegionSet.GenomicRegionSet method) closest() (GenomicRegionSet.GenomicRegionSet method) cluster() (GenomicRegionSet.GenomicRegionSet method) combine() (GenomicRegionSet.GenomicRegionSet method) complement() (GenomicRegionSet.GenomicRegionSet method) ConfigurationFile (class in Util) copy_relevent_files() (Util.Html method) correct_standard_bed_score() (Util.AuxiliaryFunctions static method) count_by_region() (GenomicRegionSet.GenomicRegionSet method) count_by_regionset() (GenomicRegionSet.GenomicRegionSet method)

count_unique_reads() (CoverageSet.CoverageSet method) counts_per_region() (GenomicRegionSet.GenomicRegionSet method) coverage_from_bam() (CoverageSet.CoverageSet method) coverage_from_bigwig() (CoverageSet.CoverageSet method) coverage_from_genomicset() (CoverageSet.CoverageSet method) coverage_per_region() (GenomicRegionSet.GenomicRegionSet method) CoverageSet (class in CoverageSet) (module) covered_by_aregion() (GenomicRegionSet.GenomicRegionSet 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) ExperimentalMatrix (class in ExperimentalMatrix) (module)

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

F

filter() (GenomicVariantSet.GenomicVariantSet method) filter_by_gene_association() (GenomicRegionSet.GenomicRegionSet method) filter_by_genes() (MotifSet.MotifSet method) filter_by_motifs() (MotifSet.MotifSet method)

filter_dbSNP() (GenomicVariantSet.GenomicVariantSet method) fix_gene_names() (AnnotationSet.AnnotationSet method) flank() (GenomicRegionSet.GenomicRegionSet method)

G

gene_association() (GenomicRegionSet.GenomicRegionSet method) GeneSet (class in GeneSet) (module) GenomeData (class in Util) GenomicRegion (class in GenomicRegion) (module) GenomicRegionSet (class in GenomicRegionSet) (module) GenomicVariant (class in GenomicVariant) (module) GenomicVariantSet (class in GenomicVariantSet) (module) get() (AnnotationSet.AnnotationSet method) get_all_genes() (GeneSet.GeneSet method) get_annotation_dump_dir() (Util.GenomeData method) get_association_file() (Util.GenomeData method) get_chrom() (GenomicRegionSet.GenomicRegionSet 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_genesets() (ExperimentalMatrix.ExperimentalMatrix method)

get_genome() (Util.GenomeData method) get_genome_data() (GenomicRegionSet.GenomicRegionSet 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_readsfiles() (ExperimentalMatrix.ExperimentalMatrix method) get_readsnames() (ExperimentalMatrix.ExperimentalMatrix method) get_regionsets() (ExperimentalMatrix.ExperimentalMatrix method) get_regionsnames() (ExperimentalMatrix.ExperimentalMatrix 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_type() (ExperimentalMatrix.ExperimentalMatrix method) get_types() (ExperimentalMatrix.ExperimentalMatrix 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) include() (GenomicRegionSet.GenomicRegionSet method) index2coordinates() (CoverageSet.CoverageSet method)

inexact_mapping() (AnnotationSet.AnnotationSet method) intersect() (GenomicRegionSet.GenomicRegionSet method) (GenomicVariantSet.GenomicVariantSet method) intersect_count() (GenomicRegionSet.GenomicRegionSet method)

J

jaccard() (GenomicRegionSet.GenomicRegionSet method)

L

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

load_objects() (ExperimentalMatrix.ExperimentalMatrix method) load_tf_list() (AnnotationSet.AnnotationSet method)

M

map_lists() (AnnotationSet.AnnotationSet method) match_ms_tags() (ExperimentalMatrix.ExperimentalMatrix method) match_suffix() (MotifSet.MotifSet method) maximum_length() (GenomicRegionSet.GenomicRegionSet method)

merge() (GenomicRegionSet.GenomicRegionSet method) Motif (class in MotifSet) MotifData (class in Util) MotifSet (class in MotifSet) (module)

N

normRPM() (CoverageSet.CoverageSet method)

O

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

OverlapType (class in Util)

P

PassThroughOptionParser (class in Util) phastCons46way_score() (CoverageSet.CoverageSet method)

projection_test() (GenomicRegionSet.GenomicRegionSet method)

R

random_regions() (GenomicRegionSet.GenomicRegionSet method) random_split() (GenomicRegionSet.GenomicRegionSet method) random_subregions() (GenomicRegionSet.GenomicRegionSet method) read() (ExperimentalMatrix.ExperimentalMatrix method) (GeneSet.GeneSet method) read_bed() (GenomicRegionSet.GenomicRegionSet method) read_bedgraph() (GenomicRegionSet.GenomicRegionSet method) read_expression() (GeneSet.GeneSet method) read_file() (MotifSet.MotifSet method)

read_motif_targets_enrichment() (MotifSet.MotifSet method) read_vcf() (GenomicVariantSet.GenomicVariantSet method) relocate_regions() (GenomicRegionSet.GenomicRegionSet method) remove_duplicates() (GenomicRegionSet.GenomicRegionSet method) remove_name() (ExperimentalMatrix.ExperimentalMatrix method) replace_region_name() (GenomicRegionSet.GenomicRegionSet method) revcomp() (Util.AuxiliaryFunctions static method)

S

scale() (CoverageSet.CoverageSet method) SequenceSet (module) SequenceType (class in Util) sort() (GenomicRegionSet.GenomicRegionSet method) (GenomicVariantSet.GenomicVariantSet method) sort_score() (GenomicRegionSet.GenomicRegionSet method)

string_is_float() (Util.AuxiliaryFunctions static method) string_is_int() (Util.AuxiliaryFunctions static method) subtract() (CoverageSet.CoverageSet method) (GeneSet.GeneSet method) (GenomicRegionSet.GenomicRegionSet method) (GenomicVariantSet.GenomicVariantSet method) subtract_aregion() (GenomicRegionSet.GenomicRegionSet method)

T

throw_error() (Util.ErrorHandler method) throw_warning() (Util.ErrorHandler method)

toString() (GenomicRegion.GenomicRegion method) total_coverage() (GenomicRegionSet.GenomicRegionSet method)

U

Util (module)

W

window() (GenomicRegionSet.GenomicRegionSet method) within_overlap() (GenomicRegionSet.GenomicRegionSet method) write() (Util.Html method) write_bed() (CoverageSet.CoverageSet method) (GenomicRegionSet.GenomicRegionSet method) write_bed_blocks() (GenomicRegionSet.GenomicRegionSet method)

write_bigwig() (CoverageSet.CoverageSet method) write_cytoscape_network() (MotifSet.MotifSet method) write_enrichment_table() (MotifSet.MotifSet method) write_vcf() (GenomicVariantSet.GenomicVariantSet method) write_wig() (CoverageSet.CoverageSet method)