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| This Release | GBrowse-2.51 | [Download] [Browse] | 18 Sep 2012 | ||||
| Latest Release | GBrowse-2.56 | [Download] [Browse] | 15 Jan 2017 | ||||
| Other Releases | |||||||
| Links | [ Discussion Forum ] [ View/Report Bugs (7) ] [ Dependencies ] [ Other Tools ] | ||||||
| CPAN Testers | FAIL (20) NA (2) [ View Reports ] [ Perl/Platform Version Matrix ] | ||||||
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| License | The Perl 5 License (Artistic 1 & GPL 1) | ||||||
| Special Files |
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| Bio::DB::GFF::Aggregator::match_gap | GFF3 match aggregator | ||
| Bio::DB::GFF::Aggregator::reftranscript | Bio::DB::GFF::Aggregator::reftranscript -- Aggregates references transcripts | 0.10 | |
| Bio::DB::GFF::Aggregator::waba_alignment | A WABA alignment | 0.20 | |
| Bio::DB::GFF::Aggregator::wormbase_gene | Wormbase gene aggregator | 0.30 | |
| Bio::DB::SeqFeature::Store::Alias | |||
| Bio::DB::SeqFeature::Store::Alias::Iterator | |||
| Bio::DB::SeqFeature::Store::Alias::Segment | |||
| Bio::DB::SeqFeature::Store::BedLoader | |||
| Bio::DB::Tagger | Simple object tagging system | 1.00 | |
| Bio::DB::Tagger::Iterator | |||
| Bio::DB::Tagger::Tag | Authored tags | ||
| Bio::DB::Tagger::mysql | |||
| Bio::Graphics::Browser2 | 2.51 | ||
| Bio::Graphics::Browser2::Action | |||
| Bio::Graphics::Browser2::AdminTracks | |||
| Bio::Graphics::Browser2::AuthorizedFeatureFile | Add HTTP authorization features to FeatureFile | ||
| Bio::Graphics::Browser2::CAlign | Compiled helper for Bio::Graphics::Browser::Realign | ||
| Bio::Graphics::Browser2::CachedTrack | |||
| Bio::Graphics::Browser2::DataBase | A simple cache for database handles | ||
| Bio::Graphics::Browser2::DataLoader | |||
| Bio::Graphics::Browser2::DataLoader::bam | |||
| Bio::Graphics::Browser2::DataLoader::bed | |||
| Bio::Graphics::Browser2::DataLoader::bigwig | |||
| Bio::Graphics::Browser2::DataLoader::featurefile | |||
| Bio::Graphics::Browser2::DataLoader::generic | |||
| Bio::Graphics::Browser2::DataLoader::gff | |||
| Bio::Graphics::Browser2::DataLoader::gff3 | |||
| Bio::Graphics::Browser2::DataLoader::sam | |||
| Bio::Graphics::Browser2::DataLoader::wig2bigwig | |||
| Bio::Graphics::Browser2::DataLoader::wiggle | |||
| Bio::Graphics::Browser2::DataSource | |||
| Bio::Graphics::Browser2::ExternalData | |||
| Bio::Graphics::Browser2::GFFhelper | Helps gbrowse plugins handle GFF | ||
| Bio::Graphics::Browser2::I18n | |||
| Bio::Graphics::Browser2::Markup | Markup routines for sequences in text form | ||
| Bio::Graphics::Browser2::MetaDB | |||
| Bio::Graphics::Browser2::MetaSegment | |||
| Bio::Graphics::Browser2::MetaSegment::Iterator | |||
| Bio::Graphics::Browser2::OptionPick | Pick options | ||
| Bio::Graphics::Browser2::PadAlignment | Insert pads into a multiple alignment | ||
| Bio::Graphics::Browser2::Plugin | Base class for gbrowse plugins. | 0.30 | |
| Bio::Graphics::Browser2::Plugin::AlignTwoSequences | a plugin that executes NCBI's bl2seq on the current view | 0.02 | |
| Bio::Graphics::Browser2::Plugin::Aligner | Dump multiple alignments from GBrowse | 0.23 | |
| Bio::Graphics::Browser2::Plugin::AttributeHiliter | hilite features based on attributes | 0.01 | |
| Bio::Graphics::Browser2::Plugin::AuthPlugin | Base class for authentication plugins | ||
| Bio::Graphics::Browser2::Plugin::BatchDumper | 1 | ||
| Bio::Graphics::Browser2::Plugin::Blat | plugin to map sequences against the genome | 0.01 | |
| Bio::Graphics::Browser2::Plugin::CMapDumper | 0.80 | ||
| Bio::Graphics::Browser2::Plugin::CreateBlastDB | a plugin that creates a Blast-formatted database from a Bio::DB::GFF database | 0.15 | |
| Bio::Graphics::Browser2::Plugin::FBTableDumper | 0.80 | ||
| Bio::Graphics::Browser2::Plugin::FastaDumper | 0.30 | ||
| Bio::Graphics::Browser2::Plugin::FilterTest | 0.O1 | ||
| Bio::Graphics::Browser2::Plugin::GeneFinder | 0.2 | ||
| Bio::Graphics::Browser2::Plugin::LDAPAuthenticate | Authenticate user against an LDAP server | ||
| Bio::Graphics::Browser2::Plugin::OligoFinder | 0.15 | ||
| Bio::Graphics::Browser2::Plugin::PamAuthenticate | Authenticate user via Pluggable Authentication Modules | ||
| Bio::Graphics::Browser2::Plugin::PrimerDesigner | a plugin to design PCR primers with primer3 | ||
| Bio::Graphics::Browser2::Plugin::ProteinDumper | A plugin for dumping translated protein sequences in various formats | 1.00 | |
| Bio::Graphics::Browser2::Plugin::RandomGene | 0.3 | ||
| Bio::Graphics::Browser2::Plugin::RestrictionAnnotator | Generate a restriction map track in GBrowse | 0.25 | |
| Bio::Graphics::Browser2::Plugin::SequenceDumper | A plugin for dumping sequences in various formats | 0.13 | |
| Bio::Graphics::Browser2::Plugin::SimpleTrackFinder | Limit list of tracks to those that match a name pattern | 0.25 | |
| Bio::Graphics::Browser2::Plugin::SinWave | 0.1 | ||
| Bio::Graphics::Browser2::Plugin::SourceTrackFinder | Limit list of tracks to those that contain arbitrary fields | 0.25 | |
| Bio::Graphics::Browser2::Plugin::Spectrogram | 1.1 | ||
| Bio::Graphics::Browser2::Plugin::Submitter | 0.1 | ||
| Bio::Graphics::Browser2::Plugin::TestAuthenticator | |||
| Bio::Graphics::Browser2::Plugin::TestFinder | |||
| Bio::Graphics::Browser2::Plugin::TrackDumper | 1.00 | ||
| Bio::Graphics::Browser2::Plugin::TrackFinder | Limit list of tracks to those that mention keywords | 0.25 | |
| Bio::Graphics::Browser2::Plugin::test | 0.10 | ||
| Bio::Graphics::Browser2::PluginSet | A set of plugins | ||
| Bio::Graphics::Browser2::Realign | Perl extension for Smith-Waterman alignments | ||
| Bio::Graphics::Browser2::Region | |||
| Bio::Graphics::Browser2::RegionSearch | Search through multiple databases for feature matches. | ||
| Bio::Graphics::Browser2::RemoteSet | A set of plugins | ||
| Bio::Graphics::Browser2::Render | |||
| Bio::Graphics::Browser2::Render::HTML | |||
| Bio::Graphics::Browser2::Render::HTML::TrackListing | |||
| Bio::Graphics::Browser2::Render::HTML::TrackListing::Categories | |||
| Bio::Graphics::Browser2::Render::Login | |||
| Bio::Graphics::Browser2::Render::Slave | |||
| Bio::Graphics::Browser2::Render::Slave::Status | |||
| Bio::Graphics::Browser2::Render::SnapshotManager | |||
| Bio::Graphics::Browser2::Render::TrackConfig | |||
| Bio::Graphics::Browser2::RenderPanels | |||
| Bio::Graphics::Browser2::SendMail | |||
| Bio::Graphics::Browser2::Session | |||
| Bio::Graphics::Browser2::Shellwords | |||
| Bio::Graphics::Browser2::SubtrackTable | |||
| Bio::Graphics::Browser2::TrackDumper | |||
| Bio::Graphics::Browser2::TrackDumper::RichSeqMaker | |||
| Bio::Graphics::Browser2::UserConf | |||
| Bio::Graphics::Browser2::UserDB | 0.5 | ||
| Bio::Graphics::Browser2::UserTracks | |||
| Bio::Graphics::Browser2::UserTracks::Database | |||
| Bio::Graphics::Browser2::UserTracks::Filesystem | |||
| Bio::Graphics::Browser2::Util | Exported utilities | ||
| Bio::Graphics::Browser::CAlign | Compiled helper for Bio::Graphics::Browser::Realign | ||
| Bio::Graphics::GBrowseFeature | |||
| Bio::Graphics::Karyotype | |||
| Bio::Graphics::Wiggle::Loader::Nosample | |||
| CGI::Toggle | Utility methods for collapsible sections | ||
| FakeHomol | |||
| GBrowseGuessDirectories | |||
| GBrowseInstall | |||
| InstallUtil | |||
| LRUCache | |||
| Legacy::DB::SyntenyBlock | |||
| Legacy::DB::SyntenyIO | |||
| Legacy::Graphics::Browser | 1.17 | ||
| Legacy::Graphics::Browser::I18n | 1.01 | ||
| Legacy::Graphics::Browser::PageSettings | |||
| Legacy::Graphics::Browser::Synteny | 0.01 | ||
| Legacy::Graphics::Browser::Util | |||
| Legacy::Graphics::BrowserConfig | |||
| MobyServices::GbrowseServices | |||
| MobyServices::b64_encoded_gif_renderer | a renderer (HTML) for b64_encoded_gif type MOBY Objects | ||
| MobyServices::b64_encoded_jpeg_renderer | a renderer (HTML) for b64_encoded_jpeg type MOBY Objects | ||
| MobyServices::text_formatted_renderer | a renderer (HTML) for text-formatted type MOBY Objects | ||
| MobyServices::text_html_renderer | a renderer (HTML) for text_html type MOBY Objects | ||
| MobyServices::text_plain_renderer | a renderer (HTML) for text_plain type MOBY Objects | ||
| MobyServices::text_xml_renderer | a renderer (HTML) for text_xml type MOBY Objects | ||
| MyFeatureFileLoader |
| Bio::Graphics::Browser::Plugin | Base class for gbrowse plugins. |
| auto_install_databases.pl | Download and install GFF data sets |
| bp_load_gff.pl | Load a Bio::DB::GFF database from GFF files. |
| cgi-bin/gbrowse_gmap | |
| docs/pod/BIOSQL_ADAPTER_HOWTO.pod | |
| docs/pod/CONFIGURE_HOWTO.pod | |
| docs/pod/CONTROLLER.pod | |
| docs/pod/DAS_HOWTO.pod | |
| docs/pod/FAQ.pod | |
| docs/pod/GBROWSE_IMG.pod | |
| docs/pod/GENBANK_HOWTO.pod | |
| docs/pod/INSTALL.MacOSX.pod | |
| docs/pod/INSTALL.pod | |
| docs/pod/MAKE_IMAGES_HOWTO.pod | |
| docs/pod/ORACLE_AND_POSTGRESQL.pod | |
| docs/pod/README-berkeley-gadfly.pod | |
| docs/pod/README-chado.pod | |
| docs/pod/README-gff-files.pod | |
| docs/pod/README-lucegene.pod | |
| gbrowse_clean.pl | Clean up sessions and other temporary gbrowse2 files |
| gbrowse_grow_cloud-vol.pl | Grow the GBrowse volume by the requested amount |
| gbrowse_key_img | |
| gbrowse_netinstall.pl | |
| gtf2gff3 | |
| load_genbank.pl | Load a Bio::DB::GFF database from GENBANK files. |
| make_das_conf.pl | Create GBrowse config files from DAS sources |
| ncbi_2_gff.pl | Massage NCBI chromosome annotation into GFF-format suitable for Bio::DB::GFF |
| process_gadfly.pl | Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser |
| process_sgd.pl | Massage SGD annotation flat files into a version suitable for the Generic Genome Browser |
| ucsc_genes2gff.pl | Convert UCSC Genome Browser-format gene files into GFF files suitable for loading into gbrowse |
| wiggle2gff3.pl |
