section 3 · Library functions 📚

178720 pages · page 52 of 894

all 3 (100762)33ssl (6156)3B (42)3G (1100)3I (51)3LIBIIO (1)3NCARG (834)3OpenMPI (1)3PVM (71)3Sympa (164)3U (96)3WN (5)3alc (212)3alleg4 (923)3alleg5 (1063)3am (31)3ast (63)3attr (4)3avr (983)3bobcat (143)3brotli (4)3bsd (239)3caca (346)3cl (1)3clc (322)3cocci (1)3coin2 (588)3coin3 (753)3coin4 (918)3compat (22)3const (18)3ctype (1)3curses (18)3cvc (2)3cxx (1060)3debug (15)3edit (1)3em (198)3embree3 (113)3embree4 (127)3erl (623)3f (128)3form (106)3freebsd (1)3fun (1)3gl (467)3gle (14)3go (1)3guile (1)3gv (7)3hal (49)3head (3)3http (66)3itcl (17)3itk (6)3iv (354)3iwidget (52)3java (1)3libmawk (10)3libunwind (29)3lua (13)3m17n (257)3m_cli2 (8)3menu (88)3monocypher (73)3nas (130)3ncurses (703)3nx (5)3o (437)3ossl (6166)3ossp (2)3p (882)3pcap (75)3perl (820)3pg13 (68)3pg14 (72)3pg15 (72)3pg16 (72)3pg17 (72)3pg18 (72)3php (1)3plplot (175)3pm (34259)3pmc (296)3posix (882)3pub (150)3python (1)3qt (832)3r (1)3readline (2)3rheolef (13)3rtapi (66)3ruby (1)3scm (459)3sharp (1)3so (8)3ssl (6930)3stap (807)3str (19)3supp (19)3t (35)3tcl (1477)3tcllib (1)3tclx (25)3tiff (60)3tk (513)3tls (13)3trf (28)3ts (239)3type (466)3valkey (395)3visa (2)3x (1069)

B (continued)

bind(3posix)bind a name to a socket✨
bind(3tk)Arrange for X events to invoke Tcl scripts✨
BIND::Conf_Parser(3pm)Parser class for BIND configuration files✨
BIND::Config::Parser(3pm)Parse BIND Config file.✨
bind_textdomain_codeset(3)set encoding of message translations✨
bindCDKObject(3)Cdk character binding capabilities✨
binders(3)✨
bindresvport(3)bind a socket to a privileged IP port✨
bindresvport(3t)bind a socket to a privileged IP port✨
bindresvport_sa(3)bind a socket to a privileged IP port✨
bindtags(3tk)Determine which bindings apply to a window, and order of evaluation✨
bindtextdomain(3)set directory containing message catalogs✨
binops(3bobcat)Template functions for class-type binary operators✨
binopsbase(3bobcat)Class template offering class-type binary operators✨
binsrch(3)general purpose functions for performing a binary search✨
binsrch(3WN)general purpose functions for performing a binary search✨
Binutils(3o)no description✨
bio(3)buffered input/output✨
Bio::Align::AlignI(3pm)An interface for describing sequence alignments.✨
Bio::Align::DNAStatistics(3pm)Calculate some statistics for a DNA alignment✨
Bio::Align::PairwiseStatistics(3pm)Base statistic object for Pairwise Alignments✨
Bio::Align::ProteinStatistics(3pm)Calculate Protein Alignment statistics (mostly distances)✨
Bio::Align::StatisticsI(3pm)Calculate some statistics for an alignment✨
Bio::Align::Utilities(3pm)A collection of utilities regarding converting and manipulating alignment objects✨
Bio::AlignIO(3pm)Handler for AlignIO Formats✨
Bio::AlignIO::arp(3pm)ARP MSA Sequence input/output stream✨
Bio::AlignIO::bl2seq(3pm)bl2seq sequence input/output stream✨
Bio::AlignIO::clustalw(3pm)clustalw sequence input/output stream✨
Bio::AlignIO::emboss(3pm)Parse EMBOSS alignment output (from applications water and needle)✨
Bio::AlignIO::fasta(3pm)fasta MSA Sequence input/output stream✨
Bio::AlignIO::Handler::GenericAlignHandler(3pm)Bio::HandlerI-based generic data handler class for alignment-based data✨
Bio::AlignIO::largemultifasta(3pm)Largemultifasta MSA Sequence input/output stream✨
Bio::AlignIO::maf(3pm)Multiple Alignment Format sequence input stream✨
Bio::AlignIO::mase(3pm)mase sequence input/output stream✨
Bio::AlignIO::mega(3pm)Parse and Create MEGA format data files✨
Bio::AlignIO::meme(3pm)meme sequence input/output stream✨
Bio::AlignIO::metafasta(3pm)Metafasta MSA Sequence input/output stream✨
Bio::AlignIO::msf(3pm)msf sequence input/output stream✨
Bio::AlignIO::nexus(3pm)NEXUS format sequence input/output stream✨
Bio::AlignIO::pfam(3pm)pfam sequence input/output stream✨
Bio::AlignIO::phylip(3pm)PHYLIP format sequence input/output stream✨
Bio::AlignIO::po(3pm)po MSA Sequence input/output stream✨
Bio::AlignIO::proda(3pm)proda sequence input/output stream This provides the basic capabilities to parse the output alignments from the ProDA multiple sequence alignment program (http://proda.stanford.edu)✨
Bio::AlignIO::prodom(3pm)prodom sequence input/output stream✨
Bio::AlignIO::psi(3pm)Read/Write PSI-BLAST profile alignment files✨
Bio::AlignIO::selex(3pm)selex sequence input/output stream✨
Bio::AlignIO::stockholm(3pm)stockholm sequence input/output stream✨
Bio::AlignIO::xmfa(3pm)XMFA MSA Sequence input/output stream✨
Bio::AnalysisI(3pm)An interface to any (local or remote) analysis tool✨
Bio::AnalysisParserI(3pm)Generic analysis output parser interface✨
Bio::AnalysisResultI(3pm)Interface for analysis result objects✨
Bio::AnnotatableI(3pm)the base interface an annotatable object must implement✨
Bio::Annotation::AnnotationFactory(3pm)Instantiates a new Bio::AnnotationI (or derived class) through a factory✨
Bio::Annotation::Collection(3pm)Default Perl implementation of AnnotationCollectionI✨
Bio::Annotation::Comment(3pm)A comment object, holding text✨
Bio::Annotation::DBLink(3pm)untyped links between databases✨
Bio::Annotation::OntologyTerm(3pm)An ontology term adapted to AnnotationI✨
Bio::Annotation::Reference(3pm)Specialised DBLink object for Literature References✨
Bio::Annotation::Relation(3pm)Relationship (pairwise) with other objects SeqI and NodeI;✨
Bio::Annotation::SimpleValue(3pm)A simple scalar✨
Bio::Annotation::StructuredValue(3pm)A scalar with embedded structured information✨
Bio::Annotation::TagTree(3pm)AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text.✨
Bio::Annotation::Target(3pm)Provides an object which represents a target (ie, a similarity hit) from one object to something in another database✨
Bio::Annotation::Tree(3pm)Provide a tree as an annotation to a Bio::AnnotatableI object✨
Bio::Annotation::TypeManager(3pm)Manages types for annotation collections✨
Bio::AnnotationCollectionI(3pm)Interface for annotation collections✨
Bio::AnnotationI(3pm)Annotation interface✨
Bio::ASN1::EntrezGene(3pm)Regular expression-based Perl Parser for NCBI Entrez Gene.✨
Bio::ASN1::EntrezGene::Indexer(3pm)Indexes NCBI Sequence files.✨
Bio::ASN1::Sequence(3pm)Regular expression-based Perl Parser for ASN.1-formatted NCBI Sequences.✨
Bio::ASN1::Sequence::Indexer(3pm)Indexes NCBI Sequence files.✨
Bio::Biblio(3pm)a bibliographic query service module✨
Bio::Biblio::Article(3pm)representation of a general article✨
Bio::Biblio::BiblioBase(3pm)an abstract base for other biblio classes✨
Bio::Biblio::Book(3pm)Representation of a book✨
Bio::Biblio::BookArticle(3pm)representation of a book article✨
Bio::Biblio::IO(3pm)Handling the bibliographic references✨
Bio::Biblio::IO::medline2ref(3pm)a converter of a raw hash to MEDLINE citations✨
Bio::Biblio::IO::medlinexml(3pm)a converter of XML files with MEDLINE citations✨
Bio::Biblio::IO::pubmed2ref(3pm)a converter of a raw hash to PUBMED citations✨
Bio::Biblio::IO::pubmedxml(3pm)a converter of XML files with PUBMED citations✨
Bio::Biblio::Journal(3pm)representation of a journal✨
Bio::Biblio::JournalArticle(3pm)representation of a journal article✨
Bio::Biblio::MedlineArticle(3pm)representation of a MEDLINE article✨
Bio::Biblio::MedlineBook(3pm)representation of a MEDLINE book✨
Bio::Biblio::MedlineBookArticle(3pm)representation of a MEDLINE book article✨
Bio::Biblio::MedlineJournal(3pm)representation of a MEDLINE journal✨
Bio::Biblio::MedlineJournalArticle(3pm)representation of a MEDLINE journal article✨
Bio::Biblio::Organisation(3pm)representation of an organisation✨
Bio::Biblio::Patent(3pm)representation of a patent✨
Bio::Biblio::Person(3pm)representation of a person✨
Bio::Biblio::Proceeding(3pm)representation of a conference proceeding✨
Bio::Biblio::Provider(3pm)representation of a general provider✨
Bio::Biblio::PubmedArticle(3pm)representation of a PUBMED article✨
Bio::Biblio::PubmedBookArticle(3pm)representation of a PUBMED book article✨
Bio::Biblio::PubmedJournalArticle(3pm)representation of a PUBMED journal article✨
Bio::Biblio::Ref(3pm)representation of a bibliographic reference✨
Bio::Biblio::Service(3pm)representation of a provider of type service✨
Bio::Biblio::TechReport(3pm)representation of a technical report✨
Bio::Biblio::Thesis(3pm)representation of thesis✨
Bio::Biblio::WebResource(3pm)representation of a web resource✨
Bio::Chado::NaturalDiversity::Reports(3pm)Collection of functions for formatting Chado stock related data✨
Bio::Chado::Schema(3pm)A standard DBIx::Class layer for the Chado database schema.✨
Bio::Chado::Schema::Test(3pm)Library to be used by Bio::Chado::Schema test scripts.✨
Bio::Chado::Schema::Util(3pm)utility functions shared by Bio::Chado::Schema objects✨
Bio::Cluster(3pm)BioPerl cluster modules✨
Bio::Cluster::ClusterFactory(3pm)Instantiates a new Bio::ClusterI (or derived class) through a factory✨
Bio::Cluster::FamilyI(3pm)Family Interface✨
Bio::Cluster::SequenceFamily(3pm)Sequence Family object✨
Bio::Cluster::UniGene(3pm)UniGene object✨
Bio::Cluster::UniGeneI(3pm)abstract interface of UniGene object✨
Bio::ClusterI(3pm)Cluster Interface✨
Bio::ClusterIO(3pm)Handler for Cluster Formats✨
Bio::ClusterIO::dbsnp(3pm)dbSNP input stream✨
Bio::ClusterIO::unigene(3pm)UniGene input stream✨
Bio::CodonUsage::IO(3pm)for reading and writing codon usage tables to file✨
Bio::CodonUsage::Table(3pm)for access to the Codon usage Database at http://www.kazusa.or.jp/codon.✨
Bio::Coordinate(3pm)Modules for working with biological coordinates✨
Bio::Coordinate::Chain(3pm)Mapping locations through a chain of coordinate mappers.✨
Bio::Coordinate::Collection(3pm)Noncontinuous match between two coordinate sets.✨
Bio::Coordinate::ExtrapolatingPair(3pm)Continuous match between two coordinate sets.✨
Bio::Coordinate::GeneMapper(3pm)Transformations between gene related coordinate systems.✨
Bio::Coordinate::Graph(3pm)Finds shortest path between nodes in a graph.✨
Bio::Coordinate::MapperI(3pm)Interface describing coordinate mappers.✨
Bio::Coordinate::Pair(3pm)Continuous match between two coordinate sets.✨
Bio::Coordinate::Result(3pm)Results from coordinate transformation.✨
Bio::Coordinate::Result::Gap(3pm)Another name for Bio::Location::Simple.✨
Bio::Coordinate::Result::Match(3pm)Another name for Bio::Location::Simple.✨
Bio::Coordinate::ResultI(3pm)Interface to identify coordinate mapper results.✨
Bio::Coordinate::Utils(3pm)Additional methods to create Bio::Coordinate objects.✨
Bio::Das::FeatureTypeI(3pm)Simple interface to Sequence Ontology feature types✨
Bio::Das::Lite(3pm)Perl extension for the DAS (HTTP+XML) Protocol (http://biodas.org/)✨
Bio::Das::SegmentI(3pm)DAS-style access to a feature database✨
Bio::DasI(3pm)DAS-style access to a feature database✨
Bio::DB::Ace(3pm)Database object interface to ACeDB servers✨
Bio::DB::Bam::Alignment(3pm)The SAM/BAM alignment object✨
Bio::DB::Bam::AlignWrapper(3pm)Add high-level methods to Bio::DB::Bam::Alignment✨
Bio::DB::Bam::Pileup(3pm)Object passed to pileup() callback✨
Bio::DB::Bam::PileupWrapper(3pm)Add high-level methods to Bio::DB::Bam::Pileup✨
Bio::DB::Bam::Query(3pm)Object representing the query portion of a BAM/SAM alignment✨
Bio::DB::Bam::Target(3pm)Object representing the query portion of a BAM/SAM alignment in NATIVE alignment✨
Bio::DB::Biblio::biofetch(3pm)a BioFetch-based access to a bibliographic citation retrieval✨
Bio::DB::Biblio::eutils(3pm)access to PubMed's bibliographic query service✨
Bio::DB::Biblio::soap(3pm)a SOAP-based access to a bibliographic query service✨
Bio::DB::BiblioI(3pm)an interface to a Bibliographic Query Service✨
Bio::DB::BioFetch(3pm)Database object interface to BioFetch retrieval✨
Bio::DB::DBFetch(3pm)Database object for retrieving using the dbfetch script✨
Bio::DB::EMBL(3pm)Database object interface for EMBL entry retrieval✨
Bio::DB::EntrezGene(3pm)Database object interface to Entrez Gene✨
Bio::DB::ESoap(3pm)Client for the NCBI Entrez EUtilities SOAP server✨
Bio::DB::ESoap::WSDL(3pm)WSDL parsing for Entrez SOAP EUtilities✨
Bio::DB::EUtilities(3pm)Webagent which interacts with and retrieves data from NCBI's eUtils.✨
Bio::DB::Failover(3pm)A Bio::DB::RandomAccessI compliant class which wraps a prioritized list of DBs✨
Bio::DB::Fasta(3pm)Fast indexed access to fasta files✨
Bio::DB::FileCache(3pm)In file cache for BioSeq objects✨
Bio::DB::Flat(3pm)Interface for indexed flat files✨
Bio::DB::Flat::BDB(3pm)Interface for BioHackathon standard BDB-indexed flat file✨
Bio::DB::Flat::BDB::embl(3pm)embl adaptor for Open-bio standard BDB-indexed flat file✨
Bio::DB::Flat::BDB::fasta(3pm)fasta adaptor for Open-bio standard BDB-indexed flat file✨
Bio::DB::Flat::BDB::genbank(3pm)genbank adaptor for Open-bio standard BDB-indexed flat file✨
Bio::DB::Flat::BDB::swiss(3pm)swissprot adaptor for Open-bio standard BDB-indexed flat file✨
Bio::DB::Flat::BinarySearch(3pm)BinarySearch search indexing system for sequence files✨
Bio::DB::GenBank(3pm)Database object interface to GenBank✨
Bio::DB::GenericWebAgent(3pm)helper base class for parameter-based remote server access and response retrieval.✨
Bio::DB::GenPept(3pm)Database object interface to GenPept✨
Bio::DB::GFF(3pm)Storage and retrieval of sequence annotation data✨
Bio::DB::GFF::Adaptor::ace(3pm)ace interface (for multiple inheritance)✨
Bio::DB::GFF::Adaptor::berkeleydb(3pm)Bio::DB::GFF database adaptor for in-memory databases✨
Bio::DB::GFF::Adaptor::berkeleydb::iterator(3pm)iterator for Bio::DB::GFF::Adaptor::berkeleydb✨
Bio::DB::GFF::Adaptor::biofetch(3pm)Cache BioFetch objects in a Bio::DB::GFF database✨
Bio::DB::GFF::Adaptor::biofetch_oracle(3pm)Cache BioFetch objects in a Bio::DB::GFF database✨
Bio::DB::GFF::Adaptor::dbi(3pm)Database adaptor for DBI (SQL) databases✨
Bio::DB::GFF::Adaptor::dbi::caching_handle(3pm)Cache for database handles✨
Bio::DB::GFF::Adaptor::dbi::iterator(3pm)iterator for Bio::DB::GFF::Adaptor::dbi✨
Bio::DB::GFF::Adaptor::dbi::mysql(3pm)Database adaptor for a specific mysql schema✨
Bio::DB::GFF::Adaptor::dbi::mysqlace(3pm)Unholy union between mysql GFF database and acedb database✨
Bio::DB::GFF::Adaptor::dbi::mysqlcmap(3pm)Database adaptor for an integraded CMap/GBrowse mysql schema✨
Bio::DB::GFF::Adaptor::dbi::mysqlopt(3pm)Deprecated database adaptor✨
Bio::DB::GFF::Adaptor::dbi::oracle(3pm)Database adaptor for a specific oracle schema✨
Bio::DB::GFF::Adaptor::dbi::oracleace(3pm)Unholy union between oracle GFF database and acedb database✨
Bio::DB::GFF::Adaptor::dbi::pg(3pm)Database adaptor for a specific postgres schema✨
Bio::DB::GFF::Adaptor::dbi::pg_fts(3pm)Database adaptor for a specific postgres schema with a TSearch2 implementation✨
Bio::DB::GFF::Adaptor::memory(3pm)Bio::DB::GFF database adaptor for in-memory databases✨
Bio::DB::GFF::Adaptor::memory::feature_serializer(3pm)utility methods for serializing and deserializing GFF features✨
Bio::DB::GFF::Adaptor::memory::iterator(3pm)iterator for Bio::DB::GFF::Adaptor::memory✨
Bio::DB::GFF::Aggregator(3pm)Aggregate GFF groups into composite features✨
Bio::DB::GFF::Aggregator::alignment(3pm)Alignment aggregator✨
Bio::DB::GFF::Aggregator::clone(3pm)Clone aggregator✨
Bio::DB::GFF::Aggregator::coding(3pm)The Coding Region Aggregator✨
Bio::DB::GFF::Aggregator::gene(3pm)Sequence Ontology Geene✨
Bio::DB::GFF::Aggregator::match(3pm)Match aggregator✨
Bio::DB::GFF::Aggregator::match_gap(3pm)GFF3 match aggregator✨
Bio::DB::GFF::Aggregator::none(3pm)No aggregation✨
Bio::DB::GFF::Aggregator::orf(3pm)An aggregator for orf regions✨
Bio::DB::GFF::Aggregator::processed_transcript(3pm)Sequence Ontology Transcript✨
Bio::DB::GFF::Aggregator::reftranscript(3pm)Aggregates references transcripts✨
Bio::DB::GFF::Aggregator::so_transcript(3pm)Sequence Ontology Transcript✨
Bio::DB::GFF::Aggregator::transcript(3pm)Transcript aggregator✨
Bio::DB::GFF::Aggregator::ucsc_acembly(3pm)UCSC acembly aggregator✨
Bio::DB::GFF::Aggregator::ucsc_ensgene(3pm)UCSC ensGene aggregator✨