Bio-EnsEMBL 113.0.0
- Released by
- ABECKER
- Version
- Release Date
- 2024-10-18
- Kwalitee
- 146.88
- Core Kwalitee
- 93.75
- LINKS
Bio-EnsEMBL 113.0.0 Latest
Kwalitee Issues
- has_tests
-
Add tests!
- no_pod_errors
-
Remove the POD errors. You can check for POD errors automatically by including Test::Pod to your test suite.
Error: Bio-EnsEMBL-113.0.0/lib/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm -- Around line 384: Unknown directive: =head Bio-EnsEMBL-113.0.0/lib/Bio/EnsEMBL/DBSQL/FastaSequenceAdaptor.pm -- Around line 144: Unknown directive: =head Bio-EnsEMBL-113.0.0/lib/Bio/EnsEMBL/External/ExternalFeatureAdaptor.pm -- Around line 35: Unknown directive: =head Bio-EnsEMBL-113.0.0/lib/Bio/EnsEMBL/IdMapping/TranscriptScoreBuilder.pm -- Around line 333: =cut found outside a pod block. Skipping to next block. Around line 344: =cut found outside a pod block. Skipping to next block. Bio-EnsEMBL-113.0.0/lib/Bio/EnsEMBL/Registry.pm -- Around line 1456: Unknown directive: =head Bio-EnsEMBL-113.0.0/lib/Bio/EnsEMBL/Transcript.pm -- Around line 2855: Unknown directive: =head Bio-EnsEMBL-113.0.0/lib/Bio/EnsEMBL/Utils/Tree/Interval/Mutable/Node.pm -- Around line 134: Unknown directive: =head
- has_tests_in_t_dir
-
Add tests or move tests.pl to the t/ directory!
- use_warnings
-
Add 'use warnings' (or its equivalents) to all modules, or convince us that your favorite module is well-known enough and people can easily see the modules warn when something bad happens.
Error: Bio::EnsEMBL::Analysis, Bio::EnsEMBL::Analysis::PairAlign, Bio::EnsEMBL::Analysis::Programs, Bio::EnsEMBL::AssemblyExceptionFeature, Bio::EnsEMBL::BaseAlignFeature, Bio::EnsEMBL::CDS, Bio::EnsEMBL::CircularSlice, Bio::EnsEMBL::DBLoader, Bio::EnsEMBL::DBSQL::AnalysisAdaptor, Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor, Bio::EnsEMBL::DBSQL::BaseAdaptor, Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor, Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor, Bio::EnsEMBL::DBSQL::BaseMetaContainer, Bio::EnsEMBL::DBSQL::DBAdaptor, Bio::EnsEMBL::DBSQL::DBConnection, Bio::EnsEMBL::DBSQL::DBEntryAdaptor, Bio::EnsEMBL::DBSQL::DensityFeatureAdaptor, Bio::EnsEMBL::DBSQL::DensityTypeAdaptor, Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor, Bio::EnsEMBL::DBSQL::ExonAdaptor, Bio::EnsEMBL::DBSQL::GeneAdaptor, Bio::EnsEMBL::DBSQL::KaryotypeBandAdaptor, Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor, Bio::EnsEMBL::DBSQL::OperonAdaptor, Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor, Bio::EnsEMBL::DBSQL::PredictionExonAdaptor, Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor, Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor, Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor, Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor, Bio::EnsEMBL::DBSQL::SeqRegionSynonymAdaptor, Bio::EnsEMBL::DBSQL::SimpleFeatureAdaptor, Bio::EnsEMBL::DBSQL::SliceAdaptor, Bio::EnsEMBL::DBSQL::StatementHandle, Bio::EnsEMBL::DBSQL::SupportingFeatureAdaptor, Bio::EnsEMBL::DBSQL::TranscriptAdaptor, Bio::EnsEMBL::DBSQL::TranscriptSupportingFeatureAdaptor, Bio::EnsEMBL::DBSQL::TranslationAdaptor, Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor, Bio::EnsEMBL::DensityPlot::BinValue, Bio::EnsEMBL::DensityPlot::BinValueSet, Bio::EnsEMBL::DnaDnaAlignFeature, Bio::EnsEMBL::DnaPepAlignFeature, Bio::EnsEMBL::Exon, Bio::EnsEMBL::ExonTranscript, Bio::EnsEMBL::External::ExternalFeatureAdaptor, Bio::EnsEMBL::FeaturePair, Bio::EnsEMBL::Gene, Bio::EnsEMBL::IdentityXref, Bio::EnsEMBL::KaryotypeBand, Bio::EnsEMBL::LRGSlice, Bio::EnsEMBL::MANE, Bio::EnsEMBL::Map::DBSQL::DitagAdaptor, Bio::EnsEMBL::Map::DBSQL::DitagFeatureAdaptor, Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor, Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor, Bio::EnsEMBL::Map::Ditag, Bio::EnsEMBL::Map::DitagFeature, Bio::EnsEMBL::Map::MapLocation, Bio::EnsEMBL::Map::Marker, Bio::EnsEMBL::Map::MarkerFeature, Bio::EnsEMBL::Map::MarkerSynonym, Bio::EnsEMBL::Mapper, Bio::EnsEMBL::Mapper::Coordinate, Bio::EnsEMBL::Mapper::Gap, Bio::EnsEMBL::Mapper::IndelCoordinate, Bio::EnsEMBL::Mapper::IndelPair, Bio::EnsEMBL::Mapper::Pair, Bio::EnsEMBL::Mapper::RangeRegistry, Bio::EnsEMBL::Mapper::Unit, Bio::EnsEMBL::MiscSet, Bio::EnsEMBL::PepDnaAlignFeature, Bio::EnsEMBL::PredictionExon, Bio::EnsEMBL::PredictionTranscript, Bio::EnsEMBL::ProteinFeature, Bio::EnsEMBL::RepeatConsensus, Bio::EnsEMBL::RepeatFeature, Bio::EnsEMBL::SeqFeature, Bio::EnsEMBL::SimpleFeature, Bio::EnsEMBL::Slice, Bio::EnsEMBL::Transcript, Bio::EnsEMBL::TranscriptFactory, Bio::EnsEMBL::Translation, Bio::EnsEMBL::UTR, Bio::EnsEMBL::Upstream, Bio::EnsEMBL::Utils::Cache, Bio::EnsEMBL::Utils::CigarString, Bio::EnsEMBL::Utils::Converter, Bio::EnsEMBL::Utils::Converter::bio_ens, Bio::EnsEMBL::Utils::Converter::bio_ens_analysis, Bio::EnsEMBL::Utils::Converter::bio_ens_exon, Bio::EnsEMBL::Utils::Converter::bio_ens_featurePair, Bio::EnsEMBL::Utils::Converter::bio_ens_gene, Bio::EnsEMBL::Utils::Converter::bio_ens_hit, Bio::EnsEMBL::Utils::Converter::bio_ens_hsp, Bio::EnsEMBL::Utils::Converter::bio_ens_predictionExon, Bio::EnsEMBL::Utils::Converter::bio_ens_predictionGene, Bio::EnsEMBL::Utils::Converter::bio_ens_seqFeature, Bio::EnsEMBL::Utils::Converter::bio_ens_transcript, Bio::EnsEMBL::Utils::Converter::ens_bio, Bio::EnsEMBL::Utils::Converter::ens_bio_featurePair, Bio::EnsEMBL::Utils::Converter::ens_bio_seqFeature, Bio::EnsEMBL::Utils::EasyArgv, Bio::EnsEMBL::Utils::Interval, Bio::EnsEMBL::Utils::PolyA, Bio::EnsEMBL::Utils::SeqDumper, Bio::EnsEMBL::Utils::SeqRegionCache, Bio::EnsEMBL::Utils::Tree::Interval::Immutable, Bio::EnsEMBL::Utils::Tree::Interval::Immutable::Node, Bio::EnsEMBL::Utils::Tree::Interval::Mutable, Bio::EnsEMBL::Utils::Tree::Interval::Mutable::Node, Bio::EnsEMBL::Utils::Tree::Interval::Mutable::PP
- meta_yml_has_provides
-
Add all modules contained in this distribution to the META.yml field 'provides'. Module::Build or Dist::Zilla::Plugin::MetaProvides do this automatically for you.
Modules
| Name | Abstract | Version | View |
|---|---|---|---|
| Bio::EnsEMBL | API to connect to and work with EnsEMBL genomic databases | 113.0 | metacpan |
| Bio::EnsEMBL::AltAlleleGroup | 113.0 | metacpan | |
| Bio::EnsEMBL::Analysis | 113.0 | metacpan | |
| Bio::EnsEMBL::Analysis::PairAlign | 113.0 | metacpan | |
| Bio::EnsEMBL::Analysis::Programs | 113.0 | metacpan | |
| Bio::EnsEMBL::ApiVersion | 113.0 | metacpan | |
| Bio::EnsEMBL::ArchiveStableId | 113.0 | metacpan | |
| Bio::EnsEMBL::AssemblyExceptionFeature | A feature that represents an assembly exception | 113.0 | metacpan |
| Bio::EnsEMBL::AssemblyMapper | 113.0 | metacpan | |
| Bio::EnsEMBL::Attribute | A generic Attribute class. | 113.0 | metacpan |
| Bio::EnsEMBL::BaseAlignFeature | Baseclass providing a common abstract implmentation for alignment features | 113.0 | metacpan |
| Bio::EnsEMBL::Biotype | 113.0 | metacpan | |
| Bio::EnsEMBL::CDS | Object representing a CDS | 113.0 | metacpan |
| Bio::EnsEMBL::ChainedAssemblyMapper | 113.0 | metacpan | |
| Bio::EnsEMBL::CircularSlice | Arbitary Slice of a genome | 113.0 | metacpan |
| Bio::EnsEMBL::CoordSystem | 113.0 | metacpan | |
| Bio::EnsEMBL::DB::ExternalFeatureFactoryI | 113.0 | metacpan | |
| Bio::EnsEMBL::DBEntry | 113.0 | metacpan | |
| Bio::EnsEMBL::DBLoader | Run time database loader | 113.0 | metacpan |
| Bio::EnsEMBL::DBSQL::AltAlleleGroupAdaptor | Adaptor for the manipulation of Alternative allele groupings | 113.0 | metacpan |
| Bio::EnsEMBL::DBSQL::AnalysisAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor | adaptor/factory for MappedSlices representing alternative assemblies | 113.0 | metacpan |
| Bio::EnsEMBL::DBSQL::AttributeAdaptor | Provides database interaction for Bio::EnsEMBL::Attribute objects. | 113.0 | metacpan |
| Bio::EnsEMBL::DBSQL::BaseAdaptor | Base Adaptor for DBSQL adaptors | 113.0 | metacpan |
| Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor | Abstract Base class for AlignFeatureAdaptors | 113.0 | metacpan |
| Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor | An Abstract Base class for all FeatureAdaptors | 113.0 | metacpan |
| Bio::EnsEMBL::DBSQL::BaseMetaContainer | Encapsulates all generic access to database meta information | 113.0 | metacpan |
| Bio::EnsEMBL::DBSQL::BaseSequenceAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::BiotypeAdaptor | An adaptor which performs database interaction relating to the storage and retrieval of Biotypes | 113.0 | metacpan |
| Bio::EnsEMBL::DBSQL::CoordSystemAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::DBAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::DBConnection | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::DBEntryAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::DataFileAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::DensityFeatureAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::DensityTypeAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor | Adaptor for DnaAlignFeatures | 113.0 | metacpan |
| Bio::EnsEMBL::DBSQL::Driver | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::Driver::Oracle | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::Driver::Pg | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::Driver::SQLite | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::Driver::Sybase | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::Driver::TestDummy | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::Driver::mysql | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::Driver::odbc | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::ExonAdaptor | An adaptor responsible for the retrieval and storage of exon objects | 113.0 | metacpan |
| Bio::EnsEMBL::DBSQL::FastaSequenceAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::GeneAdaptor | Database adaptor for the retrieval and storage of Gene objects | 113.0 | metacpan |
| Bio::EnsEMBL::DBSQL::GenomeContainer | Encapsulates all access to genome related information | 113.0 | metacpan |
| Bio::EnsEMBL::DBSQL::IntronSupportingEvidenceAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::KaryotypeBandAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::MergedAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::MetaContainer | Encapsulates all access to core database meta information | 113.0 | metacpan |
| Bio::EnsEMBL::DBSQL::MetaCoordContainer | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::MiscSetAdaptor | Provides database interaction for Bio::EnsEMBL::MiscSet objects. | 113.0 | metacpan |
| Bio::EnsEMBL::DBSQL::OntologyDBAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::OntologyTermAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::OperonAdaptor | Database adaptor for the retrieval and storage of OperonTranscript objects | 113.0 | metacpan |
| Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::PredictionExonAdaptor | Performs database interaction for PredictionExons. | 113.0 | metacpan |
| Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::ProxyDBConnection | Database connection wrapper allowing for one backing connection to be used for multiple DBs | 113.0 | metacpan |
| Bio::EnsEMBL::DBSQL::RNAProductAdaptor | Provides a means to fetch and store RNAProduct objects from a database. | 113.0 | metacpan |
| Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::SeqRegionSynonymAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::SequenceAdaptor | produce sequence strings from locations | 113.0 | metacpan |
| Bio::EnsEMBL::DBSQL::SimpleFeatureAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::SliceAdaptor | A database aware adaptor responsible for the creation of Slice objects. | 113.0 | metacpan |
| Bio::EnsEMBL::DBSQL::StatementHandle | 113.0 | metacpan | |
| Bio::EnsEMBL::DBSQL::Support::BaseCache | Base cache code | 113.0 | metacpan |
| Bio::EnsEMBL::DBSQL::Support::FullIdCache | ID based caching using all available values | 113.0 | metacpan |
| Bio::EnsEMBL::DBSQL::Support::LruIdCache | ID based caching using an LRU backed cache | 113.0 | metacpan |
| Bio::EnsEMBL::DBSQL::SupportingFeatureAdaptor | Retrieves supporting features from the database. | 113.0 | metacpan |
| Bio::EnsEMBL::DBSQL::TranscriptAdaptor | An adaptor which performs database interaction relating to the storage and retrieval of Transcripts | 113.0 | metacpan |
| Bio::EnsEMBL::DBSQL::TranscriptSupportingFeatureAdaptor | Retrieves supporting features from the database. | 113.0 | metacpan |
| Bio::EnsEMBL::DBSQL::TranslationAdaptor | Provides a means to fetch and store Translation objects from a database. | 113.0 | metacpan |
| Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::DataFile | 113.0 | metacpan | |
| Bio::EnsEMBL::DensityFeature | A feature representing a density, or precentage coverage etc. in a given region. | 113.0 | metacpan |
| Bio::EnsEMBL::DensityFeatureSet | 113.0 | metacpan | |
| Bio::EnsEMBL::DensityPlot::BinValue | 113.0 | metacpan | |
| Bio::EnsEMBL::DensityPlot::BinValueSet | 113.0 | metacpan | |
| Bio::EnsEMBL::DensityType | A type representing a density, or percentage coverage etc. in a given region. | 113.0 | metacpan |
| Bio::EnsEMBL::DnaDnaAlignFeature | Ensembl specific dna-dna pairwise alignment feature | 113.0 | metacpan |
| Bio::EnsEMBL::DnaPepAlignFeature | Ensembl specific dna-pep pairwise alignment feature | 113.0 | metacpan |
| Bio::EnsEMBL::Exon | A class representing an Exon | 113.0 | metacpan |
| Bio::EnsEMBL::ExonTranscript | An Exon feature in relation to a transcript | 113.0 | metacpan |
| Bio::EnsEMBL::External::ExternalFeatureAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::Feature | Ensembl specific sequence feature. | 113.0 | metacpan |
| Bio::EnsEMBL::FeaturePair | Stores sequence Features which are themselves hits to other sequence features. | 113.0 | metacpan |
| Bio::EnsEMBL::Gene | Object representing a genes | 113.0 | metacpan |
| Bio::EnsEMBL::Genome | A generic Genome class. | 113.0 | metacpan |
| Bio::EnsEMBL::IdMapping::Archiver | create gene_archive and peptide_archive | 113.0 | metacpan |
| Bio::EnsEMBL::IdMapping::BaseObject | base object for IdMapping objects | 113.0 | metacpan |
| Bio::EnsEMBL::IdMapping::Cache | a cache to hold data objects used by the IdMapping application | 113.0 | metacpan |
| Bio::EnsEMBL::IdMapping::Entry | object representing a ScoredMappingMatrix entry | 113.0 | metacpan |
| Bio::EnsEMBL::IdMapping::ExonScoreBuilder | 113.0 | metacpan | |
| Bio::EnsEMBL::IdMapping::GeneScoreBuilder | 113.0 | metacpan | |
| Bio::EnsEMBL::IdMapping::InternalIdMapper | 113.0 | metacpan | |
| Bio::EnsEMBL::IdMapping::InternalIdMapper::BaseMapper | 113.0 | metacpan | |
| Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblExonGeneric | 113.0 | metacpan | |
| Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblGeneGeneric | default Ensembl InternalIdMapper implementation for genes | 113.0 | metacpan |
| Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric | 113.0 | metacpan | |
| Bio::EnsEMBL::IdMapping::MappingList | object holding a list of Entries | 113.0 | metacpan |
| Bio::EnsEMBL::IdMapping::ResultAnalyser | analyse stable Id mapping results | 113.0 | metacpan |
| Bio::EnsEMBL::IdMapping::ScoreBuilder | score builder base class | 113.0 | metacpan |
| Bio::EnsEMBL::IdMapping::ScoredMappingMatrix | object holding a list of scored Entries | 113.0 | metacpan |
| Bio::EnsEMBL::IdMapping::Serialisable | base class for serialisable objects | 113.0 | metacpan |
| Bio::EnsEMBL::IdMapping::StableIdGenerator::AedesAegypti | 113.0 | metacpan | |
| Bio::EnsEMBL::IdMapping::StableIdGenerator::AnophelesGambiae | 113.0 | metacpan | |
| Bio::EnsEMBL::IdMapping::StableIdGenerator::EnsemblGeneric | default Ensembl StableIdGenerator implementation | 113.0 | metacpan |
| Bio::EnsEMBL::IdMapping::StableIdGenerator::PristionchusPacificus | 113.0 | metacpan | |
| Bio::EnsEMBL::IdMapping::StableIdMapper | 113.0 | metacpan | |
| Bio::EnsEMBL::IdMapping::SyntenyFramework | framework representing syntenic regions across the genome | 113.0 | metacpan |
| Bio::EnsEMBL::IdMapping::SyntenyRegion | object representing syntenic regions | 113.0 | metacpan |
| Bio::EnsEMBL::IdMapping::TinyExon | lightweight exon object | 113.0 | metacpan |
| Bio::EnsEMBL::IdMapping::TinyFeature | lightweight feature object | 113.0 | metacpan |
| Bio::EnsEMBL::IdMapping::TinyGene | lightweight gene object | 113.0 | metacpan |
| Bio::EnsEMBL::IdMapping::TinyTranscript | lightweight transcript object | 113.0 | metacpan |
| Bio::EnsEMBL::IdMapping::TinyTranslation | lightweight translation object | 113.0 | metacpan |
| Bio::EnsEMBL::IdMapping::TranscriptScoreBuilder | 113.0 | metacpan | |
| Bio::EnsEMBL::IdentityXref | 113.0 | metacpan | |
| Bio::EnsEMBL::Intron | 113.0 | metacpan | |
| Bio::EnsEMBL::IntronSupportingEvidence | 113.0 | metacpan | |
| Bio::EnsEMBL::KaryotypeBand | 113.0 | metacpan | |
| Bio::EnsEMBL::LRGSlice | Arbitary Slice of a genome | 113.0 | metacpan |
| Bio::EnsEMBL::MANE | Object representing a MANE transcript | 113.0 | metacpan |
| Bio::EnsEMBL::Map::DBSQL::DitagAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::Map::DBSQL::DitagFeatureAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor | 113.0 | metacpan | |
| Bio::EnsEMBL::Map::Ditag | 113.0 | metacpan | |
| Bio::EnsEMBL::Map::DitagFeature | 113.0 | metacpan | |
| Bio::EnsEMBL::Map::MapLocation | 113.0 | metacpan | |
| Bio::EnsEMBL::Map::Marker | 113.0 | metacpan | |
| Bio::EnsEMBL::Map::MarkerFeature | 113.0 | metacpan | |
| Bio::EnsEMBL::Map::MarkerSynonym | 113.0 | metacpan | |
| Bio::EnsEMBL::MappedSlice | an object representing a mapped slice | 113.0 | metacpan |
| Bio::EnsEMBL::MappedSliceContainer | container for mapped slices | 113.0 | metacpan |
| Bio::EnsEMBL::Mapper | 113.0 | metacpan | |
| Bio::EnsEMBL::Mapper::Coordinate | 113.0 | metacpan | |
| Bio::EnsEMBL::Mapper::Gap | 113.0 | metacpan | |
| Bio::EnsEMBL::Mapper::IndelCoordinate | 113.0 | metacpan | |
| Bio::EnsEMBL::Mapper::IndelPair | 113.0 | metacpan | |
| Bio::EnsEMBL::Mapper::Pair | 113.0 | metacpan | |
| Bio::EnsEMBL::Mapper::RangeRegistry | 113.0 | metacpan | |
| Bio::EnsEMBL::Mapper::Unit | One side of a map pair | 113.0 | metacpan |
| Bio::EnsEMBL::MicroRNA | A class representing a microRNA product of a transcript | 113.0 | metacpan |
| Bio::EnsEMBL::MiscFeature | A miscelaneous feature with arbitrary features and associations. | 113.0 | metacpan |
| Bio::EnsEMBL::MiscSet | This is a set representing a classification of a group of miscellaneuos features. | 113.0 | metacpan |
| Bio::EnsEMBL::OntologyTerm | 113.0 | metacpan | |
| Bio::EnsEMBL::OntologyXref | 113.0 | metacpan | |
| Bio::EnsEMBL::Operon | Object representing an operon | 113.0 | metacpan |
| Bio::EnsEMBL::OperonTranscript | Object representing a polycistronic transcript that is part of an operon | 113.0 | metacpan |
| Bio::EnsEMBL::PaddedSlice | 113.0 | metacpan | |
| Bio::EnsEMBL::PepDnaAlignFeature | Ensembl specific pep-dna pairwise alignment feature | 113.0 | metacpan |
| Bio::EnsEMBL::PredictionExon | A class representing an Exon from an ab initio prediction method | 113.0 | metacpan |
| Bio::EnsEMBL::PredictionTranscript | 113.0 | metacpan | |
| Bio::EnsEMBL::ProjectionSegment | part of the list that is returned from project function calls | 113.0 | metacpan |
| Bio::EnsEMBL::ProteinFeature | 113.0 | metacpan | |
| Bio::EnsEMBL::RNAProduct | A class representing the mature RNA product of a transcript | 113.0 | metacpan |
| Bio::EnsEMBL::Registry | 113.0 | metacpan | |
| Bio::EnsEMBL::RepeatConsensus | 113.0 | metacpan | |
| Bio::EnsEMBL::RepeatFeature | A feature representing a repeat on a piece of sequence. | 113.0 | metacpan |
| Bio::EnsEMBL::RepeatMaskedSlice | Arbitary Slice of a genome | 113.0 | metacpan |
| Bio::EnsEMBL::SeqEdit | 113.0 | metacpan | |
| Bio::EnsEMBL::SeqFeature | Ensembl specific sequence feature. | 113.0 | metacpan |
| Bio::EnsEMBL::SeqRegionSynonym | 113.0 | metacpan | |
| Bio::EnsEMBL::SimpleFeature | A simple feature with a location and label | 113.0 | metacpan |
| Bio::EnsEMBL::Slice | Arbitary Slice of a genome | 113.0 | metacpan |
| Bio::EnsEMBL::StableIdEvent | 113.0 | metacpan | |
| Bio::EnsEMBL::StableIdHistoryTree | object representing a stable ID history tree | 113.0 | metacpan |
| Bio::EnsEMBL::StopCodonReadthroughEdit | Object representing a stop codon readthrough edit in a sequence | 113.0 | metacpan |
| Bio::EnsEMBL::Storable | 113.0 | metacpan | |
| Bio::EnsEMBL::SubSlicedFeature | 113.0 | metacpan | |
| Bio::EnsEMBL::TopLevelAssemblyMapper | 113.0 | metacpan | |
| Bio::EnsEMBL::Transcript | object representing an Ensembl transcript | 113.0 | metacpan |
| Bio::EnsEMBL::TranscriptFactory | Module having the fset2transcript* subroutines | 113.0 | metacpan |
| Bio::EnsEMBL::TranscriptMapper | 113.0 | metacpan | |
| Bio::EnsEMBL::Translation | A class representing the translation of a transcript | 113.0 | metacpan |
| Bio::EnsEMBL::UTR | A UTR feature with a location and a type (five prime/3 prime) | 113.0 | metacpan |
| Bio::EnsEMBL::UnmappedObject | 113.0 | metacpan | |
| Bio::EnsEMBL::Upstream | Object that defines an upstream region | 113.0 | metacpan |
| Bio::EnsEMBL::Utils::Argument | Utility functions for argument handling | 113.0 | metacpan |
| Bio::EnsEMBL::Utils::AssemblyProjector | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::BitString | bitstring object implementation | 113.0 | metacpan |
| Bio::EnsEMBL::Utils::Cache | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::CigarString | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::CliHelper | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::ConfParser | configuration parser for perl scripts | 113.0 | metacpan |
| Bio::EnsEMBL::Utils::ConfigRegistry | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::ConversionSupport | Utility module for Vega release and schema conversion scripts | 113.0 | metacpan |
| Bio::EnsEMBL::Utils::Converter | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::Converter::bio_ens | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::Converter::bio_ens_analysis | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::Converter::bio_ens_exon | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::Converter::bio_ens_featurePair | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::Converter::bio_ens_gene | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::Converter::bio_ens_hit | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::Converter::bio_ens_hsp | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::Converter::bio_ens_predictionExon | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::Converter::bio_ens_predictionGene | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::Converter::bio_ens_seqFeature | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::Converter::bio_ens_transcript | the instance converter | 113.0 | metacpan |
| Bio::EnsEMBL::Utils::Converter::ens_bio | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::Converter::ens_bio_featurePair | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::Converter::ens_bio_seqFeature | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::EasyArgv | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::Eprof | Bespoke Ensembl profiler | 113.0 | metacpan |
| Bio::EnsEMBL::Utils::EprofStack | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::Exception | Utility functions for error handling | 113.0 | metacpan |
| Bio::EnsEMBL::Utils::IO | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::Interval | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::Iterator | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::Logger | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::Net | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::PolyA | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::Proxy | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::RNAProductTypeMapper | Utility class for mapping between RNA-product types used in the Ensembl database and respective Perl API classes. | 113.0 | metacpan |
| Bio::EnsEMBL::Utils::Scalar | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::SchemaConversion | Utility module for Vega schema conversion script | 113.0 | metacpan |
| Bio::EnsEMBL::Utils::ScriptUtils | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::SeqDumper | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::SeqRegionCache | A shared LRU cache of information about seq_regions | 113.0 | metacpan |
| Bio::EnsEMBL::Utils::Sequence | Utility functions for sequences | 113.0 | metacpan |
| Bio::EnsEMBL::Utils::Slice | Utility functions for slices | 113.0 | metacpan |
| Bio::EnsEMBL::Utils::SqlHelper | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::TranscriptSelector | Finds canonical transcripts | 113.0 | metacpan |
| Bio::EnsEMBL::Utils::Tree::Interval::Immutable | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::Tree::Interval::Immutable::Node | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::Tree::Interval::Mutable | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::Tree::Interval::Mutable::Node | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::Tree::Interval::Mutable::PP | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::URI | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::VegaCuration::Gene | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::VegaCuration::Transcript | 113.0 | metacpan | |
| Bio::EnsEMBL::Utils::VegaCuration::Translation | 113.0 | metacpan |
Provides
| Name | File | View |
|---|---|---|
| Bio::EnsEMBL::Utils::Scalar::ScopeGuard | lib/Bio/EnsEMBL/Utils/Scalar.pm | metacpan |