section 3pm · Library functions 📚

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B (continued)

Bio::DB::HTS::Tabix::Iterator(3pm)XS module wrapping around a tabix hts_itr_t✨
Bio::DB::HTS::Target(3pm)Object representing the query portion of a BAM/SAM alignment in NATIVE alignment✨
Bio::DB::HTS::VCF(3pm)Read VCF/BCF data files✨
Bio::DB::HTS::VCF::Iterator(3pm)XS module wrapping around a hts_itr_t✨
Bio::DB::IndexedBase(3pm)Base class for modules using indexed sequence files✨
Bio::DB::InMemoryCache(3pm)Abstract interface for a sequence database✨
Bio::DB::LocationI(3pm)A RandomAccessI-like abstract interface for retrieving location data from a sequence database and returning Bio::LocationI objects✨
Bio::DB::NCBIHelper(3pm)A collection of routines useful for queries to NCBI databases.✨
Bio::DB::Qual(3pm)Fast indexed access to quality files✨
Bio::DB::Query::GenBank(3pm)Build a GenBank Entrez Query✨
Bio::DB::Query::WebQuery(3pm)Helper class for web-based sequence queryies✨
Bio::DB::QueryI(3pm)Object Interface to queryable sequence databases✨
Bio::DB::RandomAccessI(3pm)Abstract interface for a sequence database✨
Bio::DB::ReferenceI(3pm)A RandomAccessI-like abstract interface for retrieving Reference data from a sequence database and returning Bio::Annotation::Reference objects✨
Bio::DB::RefSeq(3pm)Database object interface for RefSeq retrieval✨
Bio::DB::Registry(3pm)Access to the Open Bio Database Access registry scheme✨
Bio::DB::Sam(3pm)Read SAM/BAM database files✨
Bio::DB::Sam::Constants(3pm)Constants for use with SAM/BAM✨
Bio::DB::SeqFeature(3pm)Normalized feature for use with Bio::DB::SeqFeature::Store✨
Bio::DB::SeqFeature::NormalizedFeature(3pm)Normalized feature for use with Bio::DB::SeqFeature::Store✨
Bio::DB::SeqFeature::NormalizedFeatureI(3pm)Interface for normalized features✨
Bio::DB::SeqFeature::NormalizedTableFeatureI(3pm)Interface for normalized features whose hierarchy is stored in a table✨
Bio::DB::SeqFeature::Segment(3pm)Location-based access to genome annotation data✨
Bio::DB::SeqFeature::Store(3pm)Storage and retrieval of sequence annotation data✨
Bio::DB::SeqFeature::Store::Alias(3pm)override feature type, method, source and attribute fields✨
Bio::DB::SeqFeature::Store::bdb(3pm)fetch and store objects from a BerkeleyDB✨
Bio::DB::SeqFeature::Store::berkeleydb(3pm)Storage and retrieval of sequence annotation data in Berkeleydb files✨
Bio::DB::SeqFeature::Store::berkeleydb3(3pm)Storage and retrieval of sequence annotation data in Berkeleydb files✨
Bio::DB::SeqFeature::Store::DBI::Iterator(3pm)utility methods for creating and iterating over SeqFeature records✨
Bio::DB::SeqFeature::Store::DBI::MariaDB(3pm)MariaDB implementation of Bio::DB::SeqFeature::Store✨
Bio::DB::SeqFeature::Store::DBI::mysql(3pm)Mysql implementation of Bio::DB::SeqFeature::Store✨
Bio::DB::SeqFeature::Store::DBI::Pg(3pm)PostgreSQL implementation of Bio::DB::SeqFeature::Store✨
Bio::DB::SeqFeature::Store::DBI::SQLite(3pm)SQLite implementation of Bio::DB::SeqFeature::Store✨
Bio::DB::SeqFeature::Store::FeatureFileLoader(3pm)feature file loader for Bio::DB::SeqFeature::Store✨
Bio::DB::SeqFeature::Store::GFF2Loader(3pm)GFF2 file loader for Bio::DB::SeqFeature::Store✨
Bio::DB::SeqFeature::Store::GFF3Loader(3pm)GFF3 file loader for Bio::DB::SeqFeature::Store✨
Bio::DB::SeqFeature::Store::Loader(3pm)Loader✨
Bio::DB::SeqFeature::Store::LoadHelper(3pm)Internal utility for Bio::DB::SeqFeature::Store✨
Bio::DB::SeqFeature::Store::memory(3pm)In-memory implementation of Bio::DB::SeqFeature::Store✨
Bio::DB::SeqI(3pm)Abstract Interface for Sequence databases✨
Bio::DB::SoapEUtilities(3pm)Interface to the NCBI Entrez web service *BETA*✨
Bio::DB::SoapEUtilities::DocSumAdaptor(3pm)Handle for Entrez SOAP DocSums✨
Bio::DB::SoapEUtilities::FetchAdaptor(3pm)Conversion of Entrez SOAP messages to BioPerl objects✨
Bio::DB::SoapEUtilities::FetchAdaptor::seq(3pm)Fetch adaptor for 'seq' efetch SOAP messages✨
Bio::DB::SoapEUtilities::FetchAdaptor::species(3pm)Fetch adaptor for 'taxonomy' efetch SOAP messages✨
Bio::DB::SoapEUtilities::GQueryAdaptor(3pm)Handle for Entrez SOAP GlobalQuery items✨
Bio::DB::SoapEUtilities::LinkAdaptor(3pm)Handle for Entrez SOAP LinkSets✨
Bio::DB::SoapEUtilities::Result(3pm)Accessor object for SoapEUtilities results✨
Bio::DB::SwissProt(3pm)Database object interface to SwissProt retrieval✨
Bio::DB::Tagger(3pm)Simple object tagging system✨
Bio::DB::Tagger::Tag(3pm)Authored tags✨
Bio::DB::Taxonomy(3pm)Access to a taxonomy database✨
Bio::DB::Taxonomy::entrez(3pm)Taxonomy Entrez driver✨
Bio::DB::Taxonomy::flatfile(3pm)Use the NCBI taxonomy from local indexed flat files✨
Bio::DB::Taxonomy::greengenes(3pm)Use the Greengenes taxonomy✨
Bio::DB::Taxonomy::list(3pm)An implementation of Bio::DB::Taxonomy that accepts lists of words to build a database✨
Bio::DB::Taxonomy::silva(3pm)Use the Silva taxonomy✨
Bio::DB::UpdateableSeqI(3pm)An interface for writing to a database of sequences.✨
Bio::DB::WebDBSeqI(3pm)Object Interface to generalize Web Databases for retrieving sequences✨
Bio::DBLinkContainerI(3pm)Abstract interface for any object wanting to use database cross references✨
Bio::DescribableI(3pm)interface for objects with human readable names and descriptions✨
Bio::EUtilities(3pm)BioPerl low-level API for retrieving and storing data from NCBI eUtils✨
Bio::Event::EventGeneratorI(3pm)This interface describes the basic event generator class.✨
Bio::Event::EventHandlerI(3pm)An Event Handler Interface✨
Bio::Factory::AnalysisI(3pm)An interface to analysis tool factory✨
Bio::Factory::ApplicationFactoryI(3pm)Interface class for Application Factories✨
Bio::Factory::DriverFactory(3pm)Base class for factory classes loading drivers✨
Bio::Factory::EMBOSS(3pm)EMBOSS application factory class✨
Bio::Factory::FTLocationFactory(3pm)A FeatureTable Location Parser✨
Bio::Factory::LocationFactoryI(3pm)A factory interface for generating locations from a string✨
Bio::Factory::ObjectBuilderI(3pm)Interface for an object builder✨
Bio::Factory::ObjectFactory(3pm)Instantiates a new Bio::Root::RootI (or derived class) through a factory✨
Bio::Factory::ObjectFactoryI(3pm)A General object creator factory✨
Bio::Factory::SeqAnalysisParserFactory(3pm)class capable of creating SeqAnalysisParserI compliant parsers✨
Bio::Factory::SeqAnalysisParserFactoryI(3pm)interface describing objects capable of creating SeqAnalysisParserI compliant parsers✨
Bio::Factory::SequenceFactoryI(3pm)This interface allows for generic building of sequences in factories which create sequences (like SeqIO)✨
Bio::Factory::SequenceProcessorI(3pm)Interface for chained sequence processing algorithms✨
Bio::Factory::SequenceStreamI(3pm)Interface describing the basics of a Sequence Stream.✨
Bio::Factory::TreeFactoryI(3pm)Factory Interface for getting and writing trees from/to a data stream✨
Bio::FeatureHolderI(3pm)the base interface an object with features must implement✨
Bio::FeatureIO(3pm)Handler for FeatureIO✨
Bio::FeatureIO::bed(3pm)read/write features from UCSC BED format✨
Bio::FeatureIO::gff(3pm)read/write GFF feature files✨
Bio::FeatureIO::gtf(3pm)read write features in GTF format✨
Bio::FeatureIO::interpro(3pm)read features from InterPro XML✨
Bio::FeatureIO::ptt(3pm)read/write features in PTT format✨
Bio::FeatureIO::vecscreen_simple(3pm)read/write features from NCBI vecscreen -f 3 output✨
Bio::Graphics(3pm)Generate GD images of Bio::Seq objects✨
Bio::Graphics::Browser2::AuthorizedFeatureFile(3pm)Add HTTP authorization features to FeatureFile✨
Bio::Graphics::Browser2::CAlign(3pm)Compiled helper for Bio::Graphics::Browser::Realign✨
Bio::Graphics::Browser2::DataBase(3pm)A simple cache for database handles✨
Bio::Graphics::Browser2::DataLoader::archive(3pm)data loader for archives of BigWig files✨
Bio::Graphics::Browser2::DataLoader::useq(3pm)data loader for the USeq archive✨
Bio::Graphics::Browser2::DataSource(3pm)DataSource to access data✨
Bio::Graphics::Browser2::GFFhelper(3pm)Helps gbrowse plugins handle GFF✨
Bio::Graphics::Browser2::Markup(3pm)Markup routines for sequences in text form✨
Bio::Graphics::Browser2::OptionPick(3pm)Pick options✨
Bio::Graphics::Browser2::PadAlignment(3pm)Insert pads into a multiple alignment✨
Bio::Graphics::Browser2::Plugin(3pm)Base class for gbrowse plugins.✨
Bio::Graphics::Browser2::Plugin::AuthPlugin(3pm)Base class for authentication plugins✨
Bio::Graphics::Browser2::PluginSet(3pm)A set of plugins✨
Bio::Graphics::Browser2::Realign(3pm)Perl extension for Smith-Waterman alignments✨
Bio::Graphics::Browser2::Region(3pm)Provide method for fetching and manipulating regions $whole = $db->whole_segment ($segment,$settings); Given a detail segment, return the whole seq_id that contains it $region = $db->region_segment…✨
Bio::Graphics::Browser2::RegionSearch(3pm)Search through multiple databases for feature matches.✨
Bio::Graphics::Browser2::RemoteSet(3pm)A set of plugins✨
Bio::Graphics::Browser2::Render(3pm)Provide methods to render regions plugin_setting() $value = = $browser->plugin_setting("option_name"); When called in the context of a plugin, returns the setting for the requested option. The option…✨
Bio::Graphics::Browser2::Render::Slave::AWS_Balancer(3pm)✨
Bio::Graphics::Browser2::Render::Slave::Status(3pm)✨
Bio::Graphics::Browser2::RenderPanels(3pm)✨
Bio::Graphics::Browser2::Util(3pm)Exported utilities✨
Bio::Graphics::ConfiguratorI(3pm)A sectioned map of configuration options (a map of maps), with a default section. Intended to augment existing tag->value semantics (ie. of Bio::AnnotationCollectionI) for object-representation…✨
Bio::Graphics::DrawTransmembrane(3pm)draw a cartoon of an Alpha-helical transmembrane protein.✨
Bio::Graphics::Feature(3pm)A simple feature object for use with Bio::Graphics::Panel✨
Bio::Graphics::FeatureBase(3pm)Compatibility module✨
Bio::Graphics::FeatureDir(3pm)A directory of feature files and conf files✨
Bio::Graphics::FeatureFile(3pm)A set of Bio::Graphics features, stored in a file✨
Bio::Graphics::FeatureFile::Iterator(3pm)Iterator across a Bio::Graphics::FeatureFile✨
Bio::Graphics::Glyph(3pm)Base class for Bio::Graphics::Glyph objects✨
Bio::Graphics::Glyph::alignment(3pm)The "alignment" glyph✨
Bio::Graphics::Glyph::allele_tower(3pm)The "allele_tower" glyph✨
Bio::Graphics::Glyph::anchored_arrow(3pm)The "anchored_arrow" glyph✨
Bio::Graphics::Glyph::arrow(3pm)the "arrow" glyph✨
Bio::Graphics::Glyph::box(3pm)The "box" glyph✨
Bio::Graphics::Glyph::broken_line(3pm)The "broken line" glyph✨
Bio::Graphics::Glyph::cds(3pm)The "cds" glyph✨
Bio::Graphics::Glyph::christmas_arrow(3pm)The "christmas arrow" glyph✨
Bio::Graphics::Glyph::crossbox(3pm)The "crossbox" glyph✨
Bio::Graphics::Glyph::dashed_line(3pm)The "dashed line" glyph✨
Bio::Graphics::Glyph::decorated_gene(3pm)A GFF3-compatible gene glyph with protein decorations✨
Bio::Graphics::Glyph::decorated_transcript(3pm)draws processed transcript with protein decorations✨
Bio::Graphics::Glyph::diamond(3pm)The "diamond" glyph✨
Bio::Graphics::Glyph::dna(3pm)The "dna" glyph✨
Bio::Graphics::Glyph::dot(3pm)The "dot" glyph✨
Bio::Graphics::Glyph::dumbbell(3pm)A glyph that draws a "dumbbell" with the same shapes on both ends.✨
Bio::Graphics::Glyph::ellipse(3pm)The "ellipse" glyph✨
Bio::Graphics::Glyph::ex(3pm)the "ex", or "crossed box" glyph✨
Bio::Graphics::Glyph::extending_arrow(3pm)The "extending arrow" glyph✨
Bio::Graphics::Glyph::Factory(3pm)Factory for Bio::Graphics::Glyph objects✨
Bio::Graphics::Glyph::fb_shmiggle(3pm)✨
Bio::Graphics::Glyph::fixedwidth(3pm)A base class fixed width glyphs✨
Bio::Graphics::Glyph::flag(3pm)the "flag" glyph✨
Bio::Graphics::Glyph::gene(3pm)A GFF3-compatible gene glyph✨
Bio::Graphics::Glyph::generic(3pm)The "generic" glyph✨
Bio::Graphics::Glyph::graded_segments(3pm)The "graded_segments" glyph✨
Bio::Graphics::Glyph::group(3pm)The "group" glyph✨
Bio::Graphics::Glyph::hat(3pm)The "hat" glyph✨
Bio::Graphics::Glyph::heat_map(3pm)The "heat_map" glyph✨
Bio::Graphics::Glyph::heat_map_ideogram(3pm)The "heat_map_ideogram" glyph✨
Bio::Graphics::Glyph::heterogeneous_segments(3pm)The "heterogeneous_segments" glyph✨
Bio::Graphics::Glyph::hidden(3pm)The "hidden" glyph✨
Bio::Graphics::Glyph::hybrid_plot(3pm)An xyplot plot drawing dual graph using data from two or more wiggle files per track✨
Bio::Graphics::Glyph::ideogram(3pm)The "ideogram" glyph✨
Bio::Graphics::Glyph::image(3pm)A glyph that draws photographs & other images✨
Bio::Graphics::Glyph::lightning(3pm)The "lightning" glyph✨
Bio::Graphics::Glyph::line(3pm)The "line" glyph✨
Bio::Graphics::Glyph::merge_parts(3pm)a base class which suppors semantic zooming of scored alignment features✨
Bio::Graphics::Glyph::merged_alignment(3pm)The "merged_alignment" glyph✨
Bio::Graphics::Glyph::minmax(3pm)The minmax glyph✨
Bio::Graphics::Glyph::operon(3pm)The "polycistronic operon" glyph✨
Bio::Graphics::Glyph::oval(3pm)The "oval" glyph✨
Bio::Graphics::Glyph::pairplot(3pm)The "pairwise plot" glyph✨
Bio::Graphics::Glyph::pentagram(3pm)The "pentagram" glyph✨
Bio::Graphics::Glyph::phylo_align(3pm)The "phylogenetic alignment" glyph✨
Bio::Graphics::Glyph::pinsertion(3pm)The "Drosophila P-element Insertion" glyph✨
Bio::Graphics::Glyph::primers(3pm)The "STS primers" glyph✨
Bio::Graphics::Glyph::processed_transcript(3pm)The sequence ontology transcript glyph✨
Bio::Graphics::Glyph::protein(3pm)The "protein" glyph✨
Bio::Graphics::Glyph::ragged_ends(3pm)The "ragged ends" glyph✨
Bio::Graphics::Glyph::rainbow_gene(3pm)A GFF3-compatible gene glyph✨
Bio::Graphics::Glyph::redgreen_box(3pm)The "redgreen_box" glyph✨
Bio::Graphics::Glyph::redgreen_segment(3pm)The "redgreen_segments" glyph✨
Bio::Graphics::Glyph::repeating_shape(3pm)A glyph that draws the same shape repeatedly.✨
Bio::Graphics::Glyph::rndrect(3pm)The "round rect" glyph✨
Bio::Graphics::Glyph::ruler_arrow(3pm)glyph for drawing an arrow as ruler (5' and 3' are marked as label)✨
Bio::Graphics::Glyph::saw_teeth(3pm)The "saw teeth" glyph✨
Bio::Graphics::Glyph::scale(3pm)The "scale" glyph✨
Bio::Graphics::Glyph::segmented_keyglyph(3pm)The "segmented_keyglyph" glyph✨
Bio::Graphics::Glyph::segments(3pm)The "segments" glyph✨
Bio::Graphics::Glyph::so_transcript(3pm)The sequence ontology transcript glyph✨
Bio::Graphics::Glyph::span(3pm)The "span" glyph✨
Bio::Graphics::Glyph::spectrogram(3pm)The "spectrogram" glyph✨
Bio::Graphics::Glyph::splice_site(3pm)The "splice_site" glyph✨
Bio::Graphics::Glyph::stackedplot(3pm)The stackedplot glyph✨
Bio::Graphics::Glyph::ternary_plot(3pm)Draw ternary plot data✨
Bio::Graphics::Glyph::text_in_box(3pm)The "text in box" glyph✨
Bio::Graphics::Glyph::three_letters(3pm)DAS-compatible package to use for drawing a line of groups of three letters✨
Bio::Graphics::Glyph::tic_tac_toe(3pm)The "tic-tac-toe" glyph✨
Bio::Graphics::Glyph::toomany(3pm)The "too many to show" glyph✨
Bio::Graphics::Glyph::trace(3pm)A glyph that visualizes a trace file✨
Bio::Graphics::Glyph::track(3pm)The "track" glyph✨
Bio::Graphics::Glyph::transcript(3pm)The "transcript" glyph✨
Bio::Graphics::Glyph::transcript2(3pm)The "transcript2" glyph✨
Bio::Graphics::Glyph::translation(3pm)The "6-frame translation" glyph✨
Bio::Graphics::Glyph::triangle(3pm)The "triangle" glyph✨
Bio::Graphics::Glyph::two_bolts(3pm)The "two bolts" glyph✨
Bio::Graphics::Glyph::vista_plot(3pm)The "vista_plot" glyph✨
Bio::Graphics::Glyph::wave(3pm)The "wave" glyph✨
Bio::Graphics::Glyph::weighted_arrow(3pm)The "weighted arrow" glyph✨
Bio::Graphics::Glyph::whiskerplot(3pm)The whiskerplot glyph✨
Bio::Graphics::Glyph::wiggle_box(3pm)A generic box glyph compatible with dense "wig"data✨