Table of Contents - bio-ensembl-1.1.0 Documentation
Pages
Classes and Modules
- ActiveRecord
- ActiveRecord::Base
-
Ensembl
- bio-ensembl.rb
- What is it?
- ActiveRecord
- ensembl/core/collection.rb
- ensembl/core/project.rb - project calculations for Ensembl Slice
- ensembl/variation/variation.rb - Extension of ActiveRecord classes for Ensembl variation features
- ensembl/variation/variation.rb - Extension of ActiveRecord classes for Ensembl variation features
- Ensembl::Core
- Ensembl::Core::Analysis
- Ensembl::Core::AnalysisDescription
- Ensembl::Core::AssemblyException
- Ensembl::Core::AssemblyLink
- Ensembl::Core::AttribType
- Ensembl::Core::Collection
- Ensembl::Core::CoordSystem
- Ensembl::Core::DBConnection
- Ensembl::Core::DensityFeature
- Ensembl::Core::DensityType
- Ensembl::Core::Dna
- Ensembl::Core::DnaAlignFeature
- Ensembl::Core::Exon
- Ensembl::Core::ExonStableId
- Ensembl::Core::ExonSupportingFeature
- Ensembl::Core::ExonTranscript
- Ensembl::Core::ExternalDb
- Ensembl::Core::ExternalSynonym
- Ensembl::Core::Gap
- Ensembl::Core::Gene
- Ensembl::Core::GeneAttrib
- Ensembl::Core::GeneStableId
- Ensembl::Core::GoXref
- Ensembl::Core::Intron
- Ensembl::Core::Karyotype
- Ensembl::Core::Map
- Ensembl::Core::Marker
- Ensembl::Core::MarkerFeature
- Ensembl::Core::MarkerMapLocation
- Ensembl::Core::MarkerSynonym
- Ensembl::Core::Meta
- Ensembl::Core::MetaCoord
- Ensembl::Core::MiscAttrib
- Ensembl::Core::MiscFeature
- Ensembl::Core::MiscFeatureMiscSet
- Ensembl::Core::MiscSet
- Ensembl::Core::ObjectXref
- Ensembl::Core::OligoArray
- Ensembl::Core::OligoFeature
- Ensembl::Core::OligoProbe
- Ensembl::Core::PredictionExon
- Ensembl::Core::PredictionTranscript
- Ensembl::Core::ProteinAlignFeature
- Ensembl::Core::ProteinFeature
- Ensembl::Core::RegulatoryFactor
- Ensembl::Core::RegulatoryFeature
- Ensembl::Core::RepeatConsensus
- Ensembl::Core::RepeatFeature
- Ensembl::Core::SeqRegion
- Ensembl::Core::SeqRegionAttrib
- Ensembl::Core::SimpleFeature
- Ensembl::Core::Slice
- Ensembl::Core::Sliceable
- Ensembl::Core::Transcript
- Ensembl::Core::TranscriptAttrib
- Ensembl::Core::TranscriptStableId
- Ensembl::Core::TranscriptSupportingFeature
- Ensembl::Core::Translation
- Ensembl::Core::TranslationAttrib
- Ensembl::Core::TranslationStableId
- Ensembl::Core::Xref
- Ensembl::DBRegistry
- Ensembl::DBRegistry::Base
- Ensembl::DummyDBConnection
- Ensembl::Session
- Ensembl::Variation
- Ensembl::Variation::Allele
- Ensembl::Variation::AlleleGroup
- Ensembl::Variation::AlleleGroupAllele
- Ensembl::Variation::AssociateStudy
- Ensembl::Variation::AttribType
- Ensembl::Variation::CompressedGenotypeSingleBp
- Ensembl::Variation::ConsequenceMapping
- Ensembl::Variation::DBConnection
- Ensembl::Variation::FailedDescription
- Ensembl::Variation::FailedVariation
- Ensembl::Variation::FeatureType
- Ensembl::Variation::FlankingSequence
- Ensembl::Variation::Httag
- Ensembl::Variation::Individual
- Ensembl::Variation::IndividualGenotypeMultipleBp
- Ensembl::Variation::IndividualPopulation
- Ensembl::Variation::IndividualType
- Ensembl::Variation::Meta
- Ensembl::Variation::MetaCoord
- Ensembl::Variation::Phenotype
- Ensembl::Variation::PolyphenPrediction
- Ensembl::Variation::Population
- Ensembl::Variation::PopulationGenotype
- Ensembl::Variation::PopulationStructure
- Ensembl::Variation::ProteinInfo
- Ensembl::Variation::ProteinPosition
- Ensembl::Variation::ReadCoverage
- Ensembl::Variation::Sample
- Ensembl::Variation::SampleSynonym
- Ensembl::Variation::SeqRegion
- Ensembl::Variation::SiftPrediction
- Ensembl::Variation::Source
- Ensembl::Variation::StructuralVariation
- Ensembl::Variation::Study
- Ensembl::Variation::SubsnpHandle
- Ensembl::Variation::SupportingStructuralVariation
- Ensembl::Variation::TaggedVariationFeature
- Ensembl::Variation::TranscriptVariation
- Ensembl::Variation::Variation
- Ensembl::Variation::VariationAnnotation
- Ensembl::Variation::VariationFeature
- Ensembl::Variation::VariationGroup
- Ensembl::Variation::VariationGroupFeature
- Ensembl::Variation::VariationGroupVariation
- Ensembl::Variation::VariationSet
- Ensembl::Variation::VariationSetStructure
- Ensembl::Variation::VariationSetVariation
- Ensembl::Variation::VariationSynonym
Methods
- ::belongs_to_what — ActiveRecord::Base
- ::check — Ensembl::Core::Collection
- ::connect — Ensembl::DummyDBConnection
- ::connect — Ensembl::Core::DBConnection
- ::connect — Ensembl::Variation::DBConnection
- ::ensemblgenomes_connect — Ensembl::Core::DBConnection
- ::ensemblgenomes_connect — Ensembl::Variation::DBConnection
- ::fetch_all — Ensembl::Core::Slice
- ::fetch_all_by_source — Ensembl::Variation::Variation
- ::fetch_by_gene_stable_id — Ensembl::Core::Slice
- ::fetch_by_region — Ensembl::Core::Slice
- ::fetch_by_transcript_stable_id — Ensembl::Core::Slice
- ::find_all_by_attrib_type_value — Ensembl::Core::MiscFeature
- ::find_all_by_display_label — Ensembl::Core::ExternalDb
- ::find_all_by_name — Ensembl::Core::Marker
- ::find_all_by_name — Ensembl::Core::Gene
- ::find_all_by_stable_id — Ensembl::Core::Transcript
- ::find_all_coord_by_table_name — Ensembl::Core::Collection
- ::find_by_attrib_type_value — Ensembl::Core::MiscFeature
- ::find_by_display_label — Ensembl::Core::ExternalDb
- ::find_by_name — Ensembl::Core::Marker
- ::find_by_name — Ensembl::Core::Gene
- ::find_by_stable_id — Ensembl::Core::Exon
- ::find_by_stable_id — Ensembl::Core::Gene
- ::find_by_stable_id — Ensembl::Core::Translation
- ::find_by_stable_id — Ensembl::Core::Transcript
- ::find_default_by_name — Ensembl::Core::CoordSystem
- ::generic_connect — Ensembl::DBRegistry::Base
- ::get_info — Ensembl::DBRegistry::Base
- ::get_name_from_db — Ensembl::DBRegistry::Base
- ::get_species_id — Ensembl::Core::Collection
- ::has_what — ActiveRecord::Base
- ::inheritance_column — Ensembl::Core::Marker
- ::inheritance_column — Ensembl::Core::ExternalDb
- ::instance_method_already_implemented? — Ensembl::Variation::StructuralVariation
- ::new — Ensembl::Session
- ::new — Ensembl::Core::Slice
- ::new — Ensembl::Core::Gap
- ::new — Ensembl::Core::Intron
- ::species — Ensembl::Core::Collection
- #all_xrefs — Ensembl::Core::Gene
- #assembled_seq_regions — Ensembl::Core::SeqRegion
- #assembly_links_as_assembly — Ensembl::Core::SeqRegion
- #assembly_links_as_component — Ensembl::Core::SeqRegion
- #canonical_transcript — Ensembl::Core
- #cdna2genomic — Ensembl::Core::Transcript
- #cds2genomic — Ensembl::Core::Transcript
- #cds_seq — Ensembl::Core::Transcript
- #check_aa_change — Ensembl::Variation::VariationFeature
- #check_intergenic — Ensembl::Variation::VariationFeature
- #check_near_exons — Ensembl::Variation::VariationFeature
- #check_non_coding — Ensembl::Variation::VariationFeature
- #check_partial_codon — Ensembl::Variation::VariationFeature
- #check_splice_site — Ensembl::Variation::VariationFeature
- #check_upstream_downstream — Ensembl::Variation::VariationFeature
- #check_utr — Ensembl::Variation::VariationFeature
- #coding_region_cdna_end — Ensembl::Core::Transcript
- #coding_region_cdna_start — Ensembl::Core::Transcript
- #coding_region_genomic_end — Ensembl::Core::Transcript
- #coding_region_genomic_start — Ensembl::Core::Transcript
- #component_seq_regions — Ensembl::Core::SeqRegion
- #consequence_type — Ensembl::Variation::VariationFeature
- #consequence_type — Ensembl::Variation::TranscriptVariation
- #consequence_types — Ensembl::Variation::VariationFeature
- #consequence_types — Ensembl::Variation::TranscriptVariation
- #core_connection — Ensembl::Variation::VariationFeature
- #custom_transcript_variation — Ensembl::Variation::VariationFeature
- #display_label — Ensembl::Core::Gene
- #display_label — Ensembl::Core::Translation
- #display_label — Ensembl::Core::Transcript
- #display_name — Ensembl::Core::Gene
- #display_name — Ensembl::Core::Translation
- #display_name — Ensembl::Core::Slice
- #display_name — Ensembl::Core::Gap
- #display_name — Ensembl::Core::Transcript
- #dna_align_features — Ensembl::Core::Slice
- #excise — Ensembl::Core::Slice
- #exon_for_cdna_position — Ensembl::Core::Transcript
- #exon_for_genomic_position — Ensembl::Core::Transcript
- #fetch_region — Ensembl::Variation::VariationFeature
- #find_level — Ensembl::Core::CoordSystem
- #find_seqlevel — Ensembl::Core::CoordSystem
- #find_toplevel — Ensembl::Core::CoordSystem
- #five_prime_utr_seq — Ensembl::Core::Transcript
- #flanking_seq — Ensembl::Variation::VariationFeature
- #genomic2cdna — Ensembl::Core::Transcript
- #genomic2cds — Ensembl::Core::Transcript
- #genomic2pep — Ensembl::Core::Transcript
- #get_genotyped_variation_features — Ensembl::Core::Slice
- #get_objects — Ensembl::Core::Slice
- #get_structural_variations — Ensembl::Core::Slice
- #get_variation_features — Ensembl::Core::Slice
- #go_terms — Ensembl::Core::Gene
- #hgnc — Ensembl::Core::Gene
- #introns — Ensembl::Core::Transcript
- #label — Ensembl::Core::Gene
- #label — Ensembl::Core::Translation
- #label — Ensembl::Core::Transcript
- #length — Ensembl::Core::Slice
- #length — Ensembl::Core::Sliceable
- #method_missing — Ensembl::Core::Slice
- #misc_features — Ensembl::Core::Slice
- #name — Ensembl::Core::Marker
- #name — Ensembl::Core::Gene
- #name — Ensembl::Core::Map
- #name — Ensembl::Core::Translation
- #name — Ensembl::Core::Transcript
- #name_with_version — Ensembl::Core::CoordSystem
- #overlaps? — Ensembl::Core::Slice
- #pep2genomic — Ensembl::Core::Transcript
- #project — Ensembl::Core::Slice
- #project — Ensembl::Core::Sliceable
- #protein_align_features — Ensembl::Core::Slice
- #protein_seq — Ensembl::Core::Transcript
- #repeatmasked_seq — Ensembl::Core::Slice
- #reset — Ensembl::Session
- #seq — Ensembl::Core::SeqRegion
- #seq — Ensembl::Core::Exon
- #seq — Ensembl::Core::Transcript
- #seq — Ensembl::Core::Sliceable
- #seqlevel? — Ensembl::Core::CoordSystem
- #sequence — Ensembl::Core::SeqRegion
- #slice — Ensembl::Core::SeqRegion
- #slice — Ensembl::Core::Sliceable
- #somatic_status — Ensembl::Variation::Source
- #split — Ensembl::Core::Slice
- #stable_id — Ensembl::Core::Exon
- #stable_id — Ensembl::Core::Gene
- #stable_id — Ensembl::Core::Translation
- #stable_id — Ensembl::Core::Transcript
- #start — Ensembl::Core::Sliceable
- #stop — Ensembl::Core::Sliceable
- #strand — Ensembl::Core::Sliceable
- #study_type — Ensembl::Variation::Study
- #sub_slice — Ensembl::Core::Slice
- #subseq — Ensembl::Core::SeqRegion
- #subsequence — Ensembl::Core::SeqRegion
- #sv_class — Ensembl::Variation::StructuralVariation
- #three_prime_utr_seq — Ensembl::Core::Transcript
- #to_s — Ensembl::Core::MiscAttrib
- #to_s — Ensembl::Core::Xref
- #to_s — Ensembl::Core::Slice
- #toplevel? — Ensembl::Core::CoordSystem
- #transcript — Ensembl::Variation::TranscriptVariation
- #transcript_variations — Ensembl::Variation::VariationFeature
- #transform — Ensembl::Core::Sliceable
- #variation_connection — Ensembl::Core::Slice
- #within? — Ensembl::Core::Slice