All modules for which code is available
- _thread
- builtins
- common_reports_api.views
- dae.annotation.annotatable
- dae.annotation.annotate_columns
- dae.annotation.annotate_doc
- dae.annotation.annotate_schema2_parquet
- dae.annotation.annotate_utils
- dae.annotation.annotate_vcf
- dae.annotation.annotation_config
- dae.annotation.annotation_factory
- dae.annotation.annotation_pipeline
- dae.annotation.annotator_base
- dae.annotation.cnv_collection_annotator
- dae.annotation.context
- dae.annotation.debug_annotator
- dae.annotation.effect_annotator
- dae.annotation.gene_score_annotator
- dae.annotation.gene_set_annotator
- dae.annotation.liftover_annotator
- dae.annotation.normalize_allele_annotator
- dae.annotation.parquet
- dae.annotation.reannotate_instance
- dae.annotation.record_to_annotatable
- dae.annotation.score_annotator
- dae.annotation.simple_effect_annotator
- dae.common_reports.common_report
- dae.common_reports.denovo_report
- dae.common_reports.family_counter
- dae.common_reports.family_report
- dae.common_reports.generate_common_report
- dae.common_reports.people_counter
- dae.configuration.gpf_config_parser
- dae.configuration.study_config_builder
- dae.configuration.utils
- dae.conftest
- dae.dask.config
- dae.dask.named_cluster
- dae.duckdb_storage.duckdb2_variants
- dae.duckdb_storage.duckdb_connection_factory
- dae.duckdb_storage.duckdb_genotype_storage
- dae.duckdb_storage.duckdb_import_storage
- dae.duckdb_storage.duckdb_legacy_genotype_storage
- dae.duckdb_storage.duckdb_storage_config
- dae.duckdb_storage.duckdb_storage_helpers
- dae.duckdb_storage.duckdb_variants
- dae.effect_annotation.annotation_effects
- dae.effect_annotation.annotation_request
- dae.effect_annotation.annotator
- dae.effect_annotation.cli
- dae.effect_annotation.effect
- dae.effect_annotation.effect_checkers.coding
- dae.effect_annotation.effect_checkers.effect_checker
- dae.effect_annotation.effect_checkers.frame_shift
- dae.effect_annotation.effect_checkers.intron
- dae.effect_annotation.effect_checkers.promoter
- dae.effect_annotation.effect_checkers.protein_change
- dae.effect_annotation.effect_checkers.splice_site
- dae.effect_annotation.effect_checkers.start_loss
- dae.effect_annotation.effect_checkers.stop_loss
- dae.effect_annotation.effect_checkers.utr
- dae.effect_annotation.gene_codes
- dae.effect_annotation.variant
- dae.enrichment_tool.base_enrichment_background
- dae.enrichment_tool.build_coding_length_enrichment_background
- dae.enrichment_tool.build_ur_synonymous_enrichment_background
- dae.enrichment_tool.enrichment_builder
- dae.enrichment_tool.enrichment_cache_builder
- dae.enrichment_tool.enrichment_helper
- dae.enrichment_tool.enrichment_serializer
- dae.enrichment_tool.event_counters
- dae.enrichment_tool.gene_weights_background
- dae.enrichment_tool.genotype_helper
- dae.enrichment_tool.resource_implementations.enrichment_resource_impl
- dae.enrichment_tool.samocha_background
- dae.gene_profile.db
- dae.gene_profile.exporter
- dae.gene_profile.generate_gene_profile
- dae.gene_profile.statistic
- dae.gene_scores.gene_scores
- dae.gene_scores.implementations.gene_scores_impl
- dae.gene_sets.denovo_gene_set_collection
- dae.gene_sets.denovo_gene_set_helpers
- dae.gene_sets.denovo_gene_sets_config
- dae.gene_sets.denovo_gene_sets_db
- dae.gene_sets.gene_sets_db
- dae.gene_sets.gene_term
- dae.gene_sets.generate_denovo_gene_sets
- dae.genomic_resources
- dae.genomic_resources.aggregators
- dae.genomic_resources.cached_repository
- dae.genomic_resources.cli
- dae.genomic_resources.cnv_collection
- dae.genomic_resources.draw_score_histograms
- dae.genomic_resources.fsspec_protocol
- dae.genomic_resources.gene_models.gene_models
- dae.genomic_resources.gene_models.parsing
- dae.genomic_resources.gene_models.serialization
- dae.genomic_resources.genomic_context
- dae.genomic_resources.genomic_position_table.line
- dae.genomic_resources.genomic_position_table.table
- dae.genomic_resources.genomic_position_table.table_bigwig
- dae.genomic_resources.genomic_position_table.table_inmemory
- dae.genomic_resources.genomic_position_table.table_tabix
- dae.genomic_resources.genomic_position_table.table_vcf
- dae.genomic_resources.genomic_position_table.utils
- dae.genomic_resources.genomic_scores
- dae.genomic_resources.group_repository
- dae.genomic_resources.histogram
- dae.genomic_resources.implementations.annotation_pipeline_impl
- dae.genomic_resources.implementations.gene_models_impl
- dae.genomic_resources.implementations.genomic_scores_impl
- dae.genomic_resources.implementations.liftover_chain_impl
- dae.genomic_resources.implementations.reference_genome_impl
- dae.genomic_resources.liftover_chain
- dae.genomic_resources.reference_genome
- dae.genomic_resources.repository
- dae.genomic_resources.repository_factory
- dae.genomic_resources.resource_implementation
- dae.genomic_resources.statistics.base_statistic
- dae.genomic_resources.statistics.min_max
- dae.genomic_resources.testing
- dae.genomic_resources.variant_utils
- dae.genomic_scores.scores
- dae.genotype_storage
- dae.gpf_instance.gpf_instance
- dae.gpf_instance_plugin.gpf_instance_context_plugin
- dae.import_tools.cli
- dae.import_tools.import_tools
- dae.inmemory_storage.inmemory_genotype_storage
- dae.inmemory_storage.inmemory_import_storage
- dae.inmemory_storage.raw_variants
- dae.parquet.helpers
- dae.parquet.parquet_writer
- dae.parquet.partition_descriptor
- dae.parquet.schema2.parquet_io
- dae.parquet.schema2.serializers
- dae.parquet.schema2.variant_serializers
- dae.parquet_storage.storage
- dae.pedigrees.drawing
- dae.pedigrees.families_data
- dae.pedigrees.family
- dae.pedigrees.family_role_builder
- dae.pedigrees.family_tag_builder
- dae.pedigrees.generate_families_cache
- dae.pedigrees.layout
- dae.pedigrees.loader
- dae.pedigrees.pedigrees
- dae.pedigrees.testing
- dae.person_filters.person_filters
- dae.person_sets.person_sets
- dae.pheno.common
- dae.pheno.db
- dae.pheno.graphs
- dae.pheno.pheno_data
- dae.pheno.pheno_import
- dae.pheno.prepare.measure_classifier
- dae.pheno.prepare_data
- dae.pheno.registry
- dae.pheno.utils.commons
- dae.pheno.utils.lin_regress
- dae.pheno_tool.pheno_tool_adapter
- dae.pheno_tool.tool
- dae.query_variants.attributes_query
- dae.query_variants.attributes_query_inheritance
- dae.query_variants.base_query_variants
- dae.query_variants.query_runners
- dae.query_variants.sql.schema2.base_query_builder
- dae.query_variants.sql.schema2.base_variants
- dae.query_variants.sql.schema2.family_builder
- dae.query_variants.sql.schema2.sql_query_builder
- dae.query_variants.sql.schema2.summary_builder
- dae.schema2_storage.schema2_import_storage
- dae.schema2_storage.schema2_layout
- dae.studies.dataset_helpers
- dae.studies.study
- dae.studies.variants_db
- dae.task_graph.cache
- dae.task_graph.cli_tools
- dae.task_graph.demo_graphs_cli
- dae.task_graph.executor
- dae.task_graph.graph
- dae.task_graph.logging
- dae.testing.acgt_import
- dae.testing.alla_import
- dae.testing.foobar_import
- dae.testing.import_helpers
- dae.testing.setup_helpers
- dae.testing.t4c8_import
- dae.tools.annotate_variants
- dae.tools.cnv_liftover
- dae.tools.dae_liftover
- dae.tools.denovo_liftover
- dae.tools.draw_pedigree
- dae.tools.gpf_convert_study_config
- dae.tools.gpf_instance_adjustments
- dae.tools.gpf_validation_runner
- dae.tools.grr_cache_repo
- dae.tools.ped2ped
- dae.tools.phase
- dae.tools.simple_family2pedigree
- dae.tools.simple_study_import
- dae.tools.stats_liftover
- dae.tools.to_gpf_gene_models_format
- dae.tools.vcf_liftover
- dae.tools.vcfinfo_extractor
- dae.utils.cnv_utils
- dae.utils.dae_utils
- dae.utils.debug_closing
- dae.utils.dict_utils
- dae.utils.filehash
- dae.utils.fixtures
- dae.utils.fs_utils
- dae.utils.helpers
- dae.utils.progress
- dae.utils.regions
- dae.utils.sql_utils
- dae.utils.statistics
- dae.utils.variant_utils
- dae.utils.verbosity_configuration
- dae.variants.attributes
- dae.variants.core
- dae.variants.family_variant
- dae.variants.variant
- dae.variants_loaders.cnv.flexible_cnv_loader
- dae.variants_loaders.cnv.loader
- dae.variants_loaders.dae.loader
- dae.variants_loaders.parquet.loader
- dae.variants_loaders.raw.flexible_variant_loader
- dae.variants_loaders.raw.loader
- dae.variants_loaders.vcf.loader
- datasets_api.migrations.0001_initial
- datasets_api.migrations.0002_dataset_groups
- datasets_api.migrations.0003_alter_dataset_options
- datasets_api.migrations.0004_dataset_broken
- datasets_api.migrations.0005_dataset_dataset_name
- datasets_api.migrations.0006_datasethierarchy
- datasets_api.migrations.0007_datasethierarchy_direct
- datasets_api.migrations.0008_datasethierarchy_instance_id
- datasets_api.models
- datasets_api.permissions
- datasets_api.views
- enrichment_api.views
- family_api.views
- gene_profiles_api.table_views
- gene_profiles_api.views
- gene_scores.views
- gene_sets.views
- gene_view.views
- genomes_api.views
- genomic_scores_api.views
- genotype_browser.views
- gpf_instance.apps
- gpf_instance.gpf_instance
- gpf_instance.views
- gpfjs.views
- groups_api.serializers
- groups_api.views
- measures_api.views
- person_sets_api.views
- pheno_browser_api.views
- pheno_tool_api.views
- query_base.query_base
- query_state_save.migrations.0001_initial
- query_state_save.migrations.0002_auto_20190205_0736
- query_state_save.models
- query_state_save.serializers
- query_state_save.views
- sentry.views
- studies.query_transformer
- studies.response_transformer
- studies.study_wrapper
- user_queries.migrations.0001_initial
- user_queries.models
- user_queries.views
- users_api.forms
- users_api.management.commands.dataset_groups
- users_api.management.commands.dataset_mixin
- users_api.management.commands.datasets_export
- users_api.management.commands.datasets_restore
- users_api.management.commands.datasets_show
- users_api.management.commands.export_base
- users_api.management.commands.groups_cleanup
- users_api.management.commands.import_base
- users_api.management.commands.unlock_user
- users_api.management.commands.user_create
- users_api.management.commands.user_set_name
- users_api.management.commands.user_setpasswd
- users_api.management.commands.users_add
- users_api.management.commands.users_export
- users_api.management.commands.users_group_add
- users_api.management.commands.users_group_remove
- users_api.management.commands.users_remove
- users_api.management.commands.users_restore
- users_api.management.commands.users_show
- users_api.migrations.0001_initial
- users_api.migrations.0002_auto_20190424_0751
- users_api.migrations.0003_authenticationlog
- users_api.migrations.0004_resetpasswordcode_setpasswordcode_and_more
- users_api.migrations.0005_gpuserstate
- users_api.models
- users_api.serializers
- users_api.validators
- users_api.views
- utils.authentication
- utils.datasets
- utils.email_regex
- utils.expand_gene_set
- utils.gene_sets
- utils.logger
- utils.pagination
- utils.password_requirements
- utils.query_params
- utils.streaming_response_util
- utils.testing
- wdae.default_settings
- wdae.wgpf