section 3pm · Library functions 📚

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B (continued)

Bio::Graphics::Glyph::wiggle_density(3pm)A density plot compatible with dense "wig"data✨
Bio::Graphics::Glyph::wiggle_xyplot(3pm)An xyplot plot compatible with dense "wig"data✨
Bio::Graphics::Glyph::xyplot(3pm)The xyplot glyph✨
Bio::Graphics::Panel(3pm)Generate GD images of Bio::Seq objects✨
Bio::Graphics::Pictogram(3pm)generate SVG output of Pictogram display for consensus motifs✨
Bio::Graphics::RendererI(3pm)A renderer for the Bio::Graphics class that renders Bio::SeqFeature::CollectionI objects onto Bio::Graphics::Panels using configuration information provided by a Bio::Graphics::ConfiguratorI.✨
Bio::Graphics::Util(3pm)non-object-oriented utilities used in Bio::Graphics modules ($frame,$offset) = frame_and_offset($pos,$strand,$phase) Calculate the reading frame for a given genomic position, strand and phase. The…✨
Bio::Graphics::Wiggle(3pm)Binary storage for dense genomic features✨
Bio::Graphics::Wiggle::Loader(3pm)✨
Bio::HandlerBaseI(3pm)Interface class for handler methods which interact with any event-driven parsers (drivers).✨
Bio::IdCollectionI(3pm)interface for objects with multiple identifiers✨
Bio::IdentifiableI(3pm)interface for objects with identifiers✨
Bio::Index::Abstract(3pm)Abstract interface for indexing a flat file✨
Bio::Index::AbstractSeq(3pm)base class for AbstractSeq✨
Bio::Index::Blast(3pm)Indexes Blast reports and supports retrieval based on query accession(s)✨
Bio::Index::BlastTable(3pm)Indexes tabular Blast reports (-m 8 or -m 9 format) and supports retrieval based on query accession(s)✨
Bio::Index::EMBL(3pm)Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat file EMBL/Swissprot format).✨
Bio::Index::Fasta(3pm)Interface for indexing (multiple) fasta files✨
Bio::Index::Fastq(3pm)Interface for indexing (multiple) fastq files✨
Bio::Index::GenBank(3pm)Interface for indexing one or more GenBank files (i.e. flat file GenBank format).✨
Bio::Index::Hmmer(3pm)indexes HMMER reports and supports retreival based on query✨
Bio::Index::Qual(3pm)Interface for indexing (multiple) fasta qual files✨
Bio::Index::Stockholm(3pm)Interface for indexing Stockholm files✨
Bio::Index::SwissPfam(3pm)Interface for indexing swisspfam files✨
Bio::Index::Swissprot(3pm)Interface for indexing one or more Swissprot files.✨
Bio::LocatableSeq(3pm)A Bio::PrimarySeq object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq.✨
Bio::Location::Atomic(3pm)Implementation of a Atomic Location on a Sequence✨
Bio::Location::AvWithinCoordPolicy(3pm)class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise✨
Bio::Location::CoordinatePolicyI(3pm)Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location✨
Bio::Location::Fuzzy(3pm)Implementation of a Location on a Sequence which has unclear start and/or end locations✨
Bio::Location::FuzzyLocationI(3pm)Abstract interface of a Location on a Sequence which has unclear start/end location✨
Bio::Location::NarrowestCoordPolicy(3pm)class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range✨
Bio::Location::Simple(3pm)Implementation of a Simple Location on a Sequence✨
Bio::Location::Split(3pm)Implementation of a Location on a Sequence which has multiple locations (start/end points)✨
Bio::Location::SplitLocationI(3pm)Abstract interface of a Location on a Sequence which has multiple locations (start/end points)✨
Bio::Location::WidestCoordPolicy(3pm)class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range✨
Bio::LocationI(3pm)Abstract interface of a Location on a Sequence✨
Bio::MAGE(3pm)Container module for classes in the MAGE package: MAGE✨
Bio::MAGE::Array(3pm)Container module for classes in the MAGE package: Array✨
Bio::MAGE::Array::Array(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Array::ArrayGroup(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Array::ArrayManufacture(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Array::ArrayManufactureDeviation(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Array::FeatureDefect(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Array::Fiducial(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Array::ManufactureLIMS(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Array::ManufactureLIMSBiomaterial(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Array::PositionDelta(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Array::ZoneDefect(3pm)Class for the MAGE-OM API✨
Bio::MAGE::ArrayDesign(3pm)Container module for classes in the MAGE package: ArrayDesign✨
Bio::MAGE::ArrayDesign::ArrayDesign(3pm)Class for the MAGE-OM API✨
Bio::MAGE::ArrayDesign::CompositeGroup(3pm)Class for the MAGE-OM API✨
Bio::MAGE::ArrayDesign::DesignElementGroup(3pm)Class for the MAGE-OM API✨
Bio::MAGE::ArrayDesign::FeatureGroup(3pm)Class for the MAGE-OM API✨
Bio::MAGE::ArrayDesign::PhysicalArrayDesign(3pm)Class for the MAGE-OM API✨
Bio::MAGE::ArrayDesign::ReporterGroup(3pm)Class for the MAGE-OM API✨
Bio::MAGE::ArrayDesign::Zone(3pm)Class for the MAGE-OM API✨
Bio::MAGE::ArrayDesign::ZoneGroup(3pm)Class for the MAGE-OM API✨
Bio::MAGE::ArrayDesign::ZoneLayout(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Association(3pm)✨
Bio::MAGE::AuditAndSecurity(3pm)Container module for classes in the MAGE package: AuditAndSecurity✨
Bio::MAGE::AuditAndSecurity::Audit(3pm)Class for the MAGE-OM API✨
Bio::MAGE::AuditAndSecurity::Contact(3pm)Class for the MAGE-OM API✨
Bio::MAGE::AuditAndSecurity::Organization(3pm)Class for the MAGE-OM API✨
Bio::MAGE::AuditAndSecurity::Person(3pm)Class for the MAGE-OM API✨
Bio::MAGE::AuditAndSecurity::Security(3pm)Class for the MAGE-OM API✨
Bio::MAGE::AuditAndSecurity::SecurityGroup(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Base(3pm)generic base class✨
Bio::MAGE::BioAssay(3pm)Container module for classes in the MAGE package: BioAssay✨
Bio::MAGE::BioAssay::BioAssay(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioAssay::BioAssayCreation(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioAssay::BioAssayTreatment(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioAssay::Channel(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioAssay::DerivedBioAssay(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioAssay::FeatureExtraction(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioAssay::Hybridization(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioAssay::Image(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioAssay::ImageAcquisition(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioAssay::MeasuredBioAssay(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioAssay::PhysicalBioAssay(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioAssayData(3pm)Container module for classes in the MAGE package: BioAssayData✨
Bio::MAGE::BioAssayData::BioAssayData(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioAssayData::BioAssayDatum(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioAssayData::BioAssayDimension(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioAssayData::BioAssayMap(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioAssayData::BioAssayMapping(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioAssayData::BioDataCube(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioAssayData::BioDataTuples(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioAssayData::BioDataValues(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioAssayData::CompositeSequenceDimension(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioAssayData::DerivedBioAssayData(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioAssayData::DesignElementDimension(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioAssayData::DesignElementMap(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioAssayData::DesignElementMapping(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioAssayData::FeatureDimension(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioAssayData::MeasuredBioAssayData(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioAssayData::QuantitationTypeDimension(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioAssayData::QuantitationTypeMap(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioAssayData::QuantitationTypeMapping(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioAssayData::ReporterDimension(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioAssayData::Transformation(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioEvent(3pm)Container module for classes in the MAGE package: BioEvent✨
Bio::MAGE::BioEvent::BioEvent(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioEvent::Map(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioMaterial(3pm)Container module for classes in the MAGE package: BioMaterial✨
Bio::MAGE::BioMaterial::BioMaterial(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioMaterial::BioMaterialMeasurement(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioMaterial::BioSample(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioMaterial::BioSource(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioMaterial::Compound(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioMaterial::CompoundMeasurement(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioMaterial::LabeledExtract(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioMaterial::Treatment(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioSequence(3pm)Container module for classes in the MAGE package: BioSequence✨
Bio::MAGE::BioSequence::BioSequence(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioSequence::SeqFeature(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioSequence::SeqFeatureLocation(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BioSequence::SequencePosition(3pm)Class for the MAGE-OM API✨
Bio::MAGE::BQS(3pm)Container module for classes in the MAGE package: BQS✨
Bio::MAGE::BQS::BibliographicReference(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Describable(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Description(3pm)Container module for classes in the MAGE package: Description✨
Bio::MAGE::Description::Database(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Description::DatabaseEntry(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Description::Description(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Description::ExternalReference(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Description::OntologyEntry(3pm)Class for the MAGE-OM API✨
Bio::MAGE::DesignElement(3pm)Container module for classes in the MAGE package: DesignElement✨
Bio::MAGE::DesignElement::CompositeCompositeMap(3pm)Class for the MAGE-OM API✨
Bio::MAGE::DesignElement::CompositePosition(3pm)Class for the MAGE-OM API✨
Bio::MAGE::DesignElement::CompositeSequence(3pm)Class for the MAGE-OM API✨
Bio::MAGE::DesignElement::DesignElement(3pm)Class for the MAGE-OM API✨
Bio::MAGE::DesignElement::Feature(3pm)Class for the MAGE-OM API✨
Bio::MAGE::DesignElement::FeatureInformation(3pm)Class for the MAGE-OM API✨
Bio::MAGE::DesignElement::FeatureLocation(3pm)Class for the MAGE-OM API✨
Bio::MAGE::DesignElement::FeatureReporterMap(3pm)Class for the MAGE-OM API✨
Bio::MAGE::DesignElement::MismatchInformation(3pm)Class for the MAGE-OM API✨
Bio::MAGE::DesignElement::Position(3pm)Class for the MAGE-OM API✨
Bio::MAGE::DesignElement::Reporter(3pm)Class for the MAGE-OM API✨
Bio::MAGE::DesignElement::ReporterCompositeMap(3pm)Class for the MAGE-OM API✨
Bio::MAGE::DesignElement::ReporterPosition(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Experiment(3pm)Container module for classes in the MAGE package: Experiment✨
Bio::MAGE::Experiment::Experiment(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Experiment::ExperimentalFactor(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Experiment::ExperimentDesign(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Experiment::FactorValue(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Extendable(3pm)Class for the MAGE-OM API✨
Bio::MAGE::HigherLevelAnalysis(3pm)Container module for classes in the MAGE package: HigherLevelAnalysis✨
Bio::MAGE::HigherLevelAnalysis::BioAssayDataCluster(3pm)Class for the MAGE-OM API✨
Bio::MAGE::HigherLevelAnalysis::Node(3pm)Class for the MAGE-OM API✨
Bio::MAGE::HigherLevelAnalysis::NodeContents(3pm)Class for the MAGE-OM API✨
Bio::MAGE::HigherLevelAnalysis::NodeValue(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Identifiable(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Measurement(3pm)Container module for classes in the MAGE package: Measurement✨
Bio::MAGE::Measurement::ConcentrationUnit(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Measurement::DistanceUnit(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Measurement::MassUnit(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Measurement::Measurement(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Measurement::QuantityUnit(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Measurement::TemperatureUnit(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Measurement::TimeUnit(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Measurement::Unit(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Measurement::VolumeUnit(3pm)Class for the MAGE-OM API✨
Bio::MAGE::NameValueType(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Protocol(3pm)Container module for classes in the MAGE package: Protocol✨
Bio::MAGE::Protocol::Hardware(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Protocol::HardwareApplication(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Protocol::Parameter(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Protocol::Parameterizable(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Protocol::ParameterizableApplication(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Protocol::ParameterValue(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Protocol::Protocol(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Protocol::ProtocolApplication(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Protocol::Software(3pm)Class for the MAGE-OM API✨
Bio::MAGE::Protocol::SoftwareApplication(3pm)Class for the MAGE-OM API✨
Bio::MAGE::QuantitationType(3pm)Container module for classes in the MAGE package: QuantitationType✨
Bio::MAGE::QuantitationType::ConfidenceIndicator(3pm)Class for the MAGE-OM API✨
Bio::MAGE::QuantitationType::DerivedSignal(3pm)Class for the MAGE-OM API✨
Bio::MAGE::QuantitationType::Error(3pm)Class for the MAGE-OM API✨
Bio::MAGE::QuantitationType::ExpectedValue(3pm)Class for the MAGE-OM API✨
Bio::MAGE::QuantitationType::Failed(3pm)Class for the MAGE-OM API✨
Bio::MAGE::QuantitationType::MeasuredSignal(3pm)Class for the MAGE-OM API✨
Bio::MAGE::QuantitationType::PresentAbsent(3pm)Class for the MAGE-OM API✨
Bio::MAGE::QuantitationType::PValue(3pm)Class for the MAGE-OM API✨
Bio::MAGE::QuantitationType::QuantitationType(3pm)Class for the MAGE-OM API✨
Bio::MAGE::QuantitationType::Ratio(3pm)Class for the MAGE-OM API✨
Bio::MAGE::QuantitationType::SpecializedQuantitationType(3pm)Class for the MAGE-OM API✨
Bio::MAGE::QuantitationType::StandardQuantitationType(3pm)Class for the MAGE-OM API✨
Bio::MAGE::SQLUtils(3pm)a module for exporting MAGE-OM objects to a database✨
Bio::MAGE::Tools::MGEDOntologyClassEntry(3pm)✨
Bio::MAGE::Tools::MGEDOntologyEntry(3pm)✨
Bio::MAGE::Tools::MGEDOntologyHelper(3pm)✨
Bio::MAGE::Tools::MGEDOntologyPropertyEntry(3pm)✨
Bio::MAGE::XML::Handler(3pm)✨
Bio::MAGE::XML::Handler::ObjectHandler::SQL(3pm)DESCRIPTION of Object✨
Bio::MAGE::XML::Handler::ObjectHandlerI(3pm)Abstract class for processing Bio::MAGE objects.✨
Bio::MAGE::XML::Reader(3pm)a module for exporting MAGE-ML✨
Bio::MAGE::XML::Writer(3pm)a module for exporting MAGE-ML✨
Bio::Matrix::Generic(3pm)A generic matrix implementation✨
Bio::Matrix::IO(3pm)A factory for Matrix parsing✨