📦 gbrowse

51 pages

B

bed2gff3(1p)Convert UCSC Genome Browser-format gene files into GFF files suitable for loading into gbrowse✨
Bio::DB::GFF::Aggregator::match_gap(3pm)GFF3 match aggregator✨
Bio::DB::GFF::Aggregator::reftranscript(3pm)Aggregates references transcripts✨
Bio::DB::GFF::Aggregator::waba_alignment(3pm)A WABA alignment✨
Bio::DB::GFF::Aggregator::wormbase_gene(3pm)Wormbase gene aggregator✨
Bio::DB::SeqFeature::Store::Alias(3pm)override feature type, method, source and attribute fields✨
Bio::DB::Tagger(3pm)Simple object tagging system✨
Bio::DB::Tagger::Tag(3pm)Authored tags✨
Bio::Graphics::Browser2::AuthorizedFeatureFile(3pm)Add HTTP authorization features to FeatureFile✨
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✨

C

CGI::Toggle(3pm)Utility methods for collapsible sections✨

G

gbrowse(1)The Generic Genome Browser✨
GBrowse::ConfigData(3pm)Configuration for GBrowse✨
gbrowse_aws_balancer(1p)Load balance GBrowse using Amazon Web Service instances✨
gbrowse_change_passwd(1)Modify a gbrowse user password✨
gbrowse_clean(1p)Clean up sessions and other temporary gbrowse2 files✨
gbrowse_create_account(1)Creates an account for GBrowse✨
gbrowse_grow_cloud_vol(1p)Grow the GBrowse volume by the requested amount✨
gbrowse_import_ucsc_db(1)Creates a framework data source✨
gbrowse_metadb_config(1)Initializes an empty GBrowse user accounts and uploads metadata database✨
gbrowse_set_admin_passwd(1)Sets the administrator password for the GBrowse admin✨
gbrowse_slave(1)Creates an account for GBrowse✨
gbrowse_syn_load_alignment_database(1)Script to load the database for gbrowse_syn✨
gbrowse_syn_load_alignments_msa(1)Script to load the database for gbrowse_syn from alignement file✨
gbrowse_sync_aws_slave(1p)Synchronize local file system to GBrowse slave volume.✨
gtf2gff3(1p)Converts GTF formatted files to valid GFF3 files✨

L

Legacy::Graphics::Browser(3pm)✨
load_genbank(1p)Load a Bio::DB::GFF database from GENBANK files.✨

M

make_das_conf(1p)Create GBrowse config files from DAS sources✨

S

scan_gbrowse(1)Scan the gbrowse2 instance for discoverable tracks✨

U

ucsc_genes2gff(1p)Convert UCSC Genome Browser-format gene files into GFF files suitable for loading into gbrowse✨

W

wiggle2gff3(1p)Converts UCSC WIG format files into gff3 files✨