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DEPRECATED.md

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Ensembl Funcgen Deprecated Methods

This file contains the list of methods, modules and scripts deprecated in the Ensembl Funcgen API. A method is deprecated when it is not functional any more (schema/data change) or has been replaced by a better one. Backwards compatibility is provided whenever possible. When a method is deprecated, a deprecation warning is thrown whenever the method is used. The warning also contains instructions on replacing the deprecated method and when it will be removed. A year after deprecation (4 Ensembl releases), the method is removed from the API.

Removed in Ensembl Release 88

  • Bio::Ensembl::Funcgen::Channel
  • Bio::Ensembl::Funcgen::DBSQL::ChannelAdaptor
  • Bio::Ensembl::Funcgen::ExperimentalChip
  • Bio::Ensembl::Funcgen::DBSQL::ExperimentalChipAdaptor
  • Bio::Ensembl::Funcgen::InputSet
  • Bio::Ensembl::Funcgen::DBSQL::InputSetAdaptor
  • Bio::Ensembl::Funcgen::ResultFeature
  • Bio::Ensembl::Funcgen::DBSQL::ResultFeatureAdaptor
  • Bio::Ensembl::Funcgen::Collector::ResultFeature

Removed in Ensembl Release 85

  • Bio::Ensembl::Funcgen::Experiment::date()
  • Bio::Ensembl::Funcgen::ResultSet::get_replicate_set_by_chip_channel_id()
  • Bio::Ensembl::Funcgen::DBSQL::BaseAdaptor::list_dbIDs()
  • Bio::Ensembl::Funcgen::DBSQL::BaseAdaptor::_constrain_status()
  • Bio::Ensembl::Funcgen::DBSQL::BaseAdaptor::fetch_all_by_status()
  • Bio::Ensembl::Funcgen::DBSQL::DBEntryAdaptor::list_regulatory_feature_ids_by_extid()
  • Bio::Ensembl::Funcgen::DBSQL::DBEntryAdaptor::list_probeset_ids_by_extid()
  • Bio::Ensembl::Funcgen::DBSQL::DBEntryAdaptor::list_feature_type_ids_by_extid()
  • Bio::Ensembl::Funcgen::DBSQL::DBEntryAdaptor::list_external_feature_ids_by_extid()
  • Bio::Ensembl::Funcgen::DBSQL::DBEntryAdaptor::list_annotated_feature_ids_by_extid()
  • Bio::Ensembl::Funcgen::DBSQL::DBEntryAdaptor::list_probe_ids_by_extid()
  • Bio::Ensembl::Funcgen::DBSQL::FeatureSetAdaptor::fetch_all_by_type()
  • Bio::Ensembl::Funcgen::DBSQL::InputSubsetAdaptor::fetch_by_name_and_experiment()
  • Bio::Ensembl::Funcgen::DBSQL::ProbeFeatureAdaptor::fetch_all_by_probeset()
  • Bio::Ensembl::Funcgen::DBSQL::ResultFeatureAdaptor::fetch_all()
  • Bio::Ensembl::Funcgen::DBSQL::ResultSetAdaptor::store_dbfile_data_dir()
  • Bio::Ensembl::Funcgen::DBSQL::ResultSetAdaptor::_fetch_dbfile_data_dir()

Removed in Ensembl Release 84

  • Bio::Ensembl::Funcgen::Dataset::add_supporting_sets()

  • Bio::Ensembl::Funcgen::Dataset::_validate_and_set_types()

  • Bio::Ensembl::Funcgen::InputSubset::input_set()

  • Bio::Ensembl::Funcgen::InputSubset::archive_id()

  • Bio::Ensembl::Funcgen::InputSubset::display_url()

  • Bio::Ensembl::Funcgen::Probe::add_Analysis_score()

  • Bio::Ensembl::Funcgen::Probe::add_Analysis_CoordSystem_score()

  • Bio::Ensembl::Funcgen::Probe::get_score_by_Analysis()

  • Bio::Ensembl::Funcgen::Probe::get_score_by_Analysis_CoordSystem()

  • Bio::Ensembl::Funcgen::Probe::get_all_design_scores()

  • Bio::Ensembl::Funcgen::DBSQL::DataSetAdaptor::store_updated_sets()

  • Bio::Ensembl::Funcgen::HiveConfig::Alignment_conf.pm

  • Bio::Ensembl::Funcgen::HiveConfig::Peaks_conf.pm

  • Bio::Ensembl::Funcgen::HiveConfig::Annotation_conf.pm

  • Bio::Ensembl::Funcgen::HiveConfig::Dnase_profile_conf.pm

  • Bio::Ensembl::Funcgen::HiveConfig::MotifFinder_conf.pm

  • Bio::EnsEMBL::Funcgen::RunnableDB::Alignment.pm

  • Bio::EnsEMBL::Funcgen::RunnableDB::AnnotateRegulatoryFeatures.pm

  • Bio::EnsEMBL::Funcgen::RunnableDB::Annotation.pm

  • Bio::EnsEMBL::Funcgen::RunnableDB::ClusterMotifs.pm

  • Bio::EnsEMBL::Funcgen::RunnableDB::ConvergeReplicates.pm

  • Bio::EnsEMBL::Funcgen::RunnableDB::Funcgen.pm

  • Bio::EnsEMBL::Funcgen::RunnableDB::Import.pm

  • Bio::EnsEMBL::Funcgen::RunnableDB::InferMotifs.pm

  • Bio::EnsEMBL::Funcgen::RunnableDB::MakeDnaseProfile.pm

  • Bio::EnsEMBL::Funcgen::RunnableDB::Motif.pm

  • Bio::EnsEMBL::Funcgen::RunnableDB::RunBWA.pm

  • Bio::EnsEMBL::Funcgen::RunnableDB::RunCCAT.pm

  • Bio::EnsEMBL::Funcgen::RunnableDB::RunCentipede.pm

  • Bio::EnsEMBL::Funcgen::RunnableDB::RunMACS.pm

  • Bio::EnsEMBL::Funcgen::RunnableDB::RunSWEmbl.pm

  • Bio::EnsEMBL::Funcgen::RunnableDB::SWEmbl.pm

  • Bio::EnsEMBL::Funcgen::RunnableDB::SetupAlignmentPipeline.pm

  • Bio::EnsEMBL::Funcgen::RunnableDB::SetupAnnotationPipeline.pm

  • Bio::EnsEMBL::Funcgen::RunnableDB::SetupMotifInference.pm

  • Bio::EnsEMBL::Funcgen::RunnableDB::SetupPeaksPipeline.pm

  • Bio::EnsEMBL::Funcgen::RunnableDB::WrapUpAlignment.pm

  • scripts/pipeline/configure_hive.pl

  • scripts/regulatory_build/load_segmentation.pl

  • scripts/regulatory_build/unpack_swilder_segmentation.pl