TOC for ensembl::modules::Bio::EnsEMBL
AffyArrayA module to represent an Affymetrix array.
AffyFeatureA module to represent an Affy probe's genomic mapping.
AffyProbeA module to represent an Affymetrix probe.
AlignStrainSliceRepresents the slice of the genome aligned with certain strains (applying the variations/indels)
AnalysisStores details of an analysis run
ArchiveStableIdBio::EnsEMBL::ArchiveStableId
AssemblyExceptionFeatureA feature that represents an assembly exception
AssemblyMapperHandles mapping between two coordinate systems using the information stored in the assembly table.
AttributeA generic Attribute class.
BaseAlignFeatureBaseclass providing a common abstract implmentation for alignment features
ChainedAssemblyMapperHandles mapping between two coordinate systems using the information stored in the assembly table
CollectionAbstract base class for feature collection classes.
CoordSystemBio::EnsEMBL::CoordSystem
DBEntryObject representing an external reference (xref)
DBLoaderRun time database loader
DensityFeatureA feature representing a density, or precentage coverage etc. in a given region.
DensityFeatureSetA feature representing a set of density features
DensityTypeA type representing a density, or percentage coverage etc. in a given region.
DnaDnaAlignFeatureEnsembl specific dna-dna pairwise alignment feature
DnaPepAlignFeatureEnsembl specific dna-pep pairwise alignment feature
ExonA class representing an Exon
FeatureEnsembl specific sequence feature.
FeaturePairStores sequence Features which are themselves hits to other sequence features.
GeneObject representing a genes
GoXrefBio::EnsEMBL::GoXref
IdentityXrefBio::EnsEMBL::IdentityXref
IndividualSliceSubClass of the Slice. Represents the slice of the genome for a certain individual (applying the alleles for this individual)
IndividualSliceFactory
Intron
KaryotypeBandBio::EnsEMBL::DBSQL::KaryotypeBand
MappedSlicean object representing a mapped slice
MappedSliceContainercontainer for mapped slices
MapperBio::EnsEMBL::Mapper
MiscFeatureA miscelaneous feature with arbitrary features and associations.
MiscSetThis is a set representing a classification of a group of miscellaneuos features.
OligoArrayA module to represent an oligonucleotide microarray.
OligoFeatureA module to represent an oligonucleotide probe's genomic mapping.
OligoProbeA module to represent an oligonucleotide probe.
OntologyTermBio::EnsEMBL::OntologyTerm
PepDnaAlignFeatureEnsembl specific pep-dna pairwise alignment feature
PredictionExonA class representing an Exon from an ab initio prediction method
PredictionTranscriptPredictionTranscript
ProjectionSegmentpart of the list that is returned from project function calls
ProteinFeatureBio::EnsEMBL::ProteinFeature
RegistryBio::EnsEMBL::Registry
RepeatConsensus
RepeatFeatureA feature representing a repeat on a piece of sequence.
RepeatMaskedSliceArbitary Slice of a genome
RootBio::EnsEMBL::Root
SNPBio::EnsEMBL::SNP
SeqEditA class representing a post transcriptional edit to a sequence.
SeqFeatureEnsembl specific sequence feature.
SeqFeatureIBio::EnsEMBL::SeqFeatureI
SimpleFeatureA simple feature with a location and label
SliceArbitary Slice of a genome
StableIdEventobject representing a stable ID mapping event
StableIdHistoryTreeobject representing a stable ID history tree
StorableBio::EnsEMBL::Storable
StrainSliceSubClass of the Slice. Represents the slice of the genome for a certain strain (applying the variations)
TopLevelAssemblyMapperHandles mapping between a given coordinate system and the toplevel pseudo coordinate system.
Transcriptobject representing an Ensembl transcript
TranscriptFactoryModule having the fset2transcript* subroutines
TranscriptMapperA utility class used to perform coordinate conversions between a number of coordinate systems relating to transcripts
TranslationA class representing the translation of a transcript
UnconventionalTranscriptAssociationA class representing an some sort of unconventional association between a gene and a transcript.
UnmappedObjectA object representing why a particular entity was NOT mapped to the ensembl.
UpstreamObject that defines an upstream region