All modules for which code is available
- builtins
- gain.annotation.allele_score_annotator
- gain.annotation.annotatable
- gain.annotation.annotate_columns
- gain.annotation.annotate_doc
- gain.annotation.annotate_tabular
- gain.annotation.annotate_utils
- gain.annotation.annotate_vcf
- gain.annotation.annotation_config
- gain.annotation.annotation_factory
- gain.annotation.annotation_genomic_context_cli
- gain.annotation.annotation_pipeline
- gain.annotation.annotator_base
- gain.annotation.chrom_mapping_annotator
- gain.annotation.debug_annotator
- gain.annotation.docker_annotator
- gain.annotation.effect_annotator
- gain.annotation.fragment_score_annotator
- gain.annotation.gene_score_annotator
- gain.annotation.gene_set_annotator
- gain.annotation.genomic_score_annotator_base
- gain.annotation.liftover_annotator
- gain.annotation.normalize_allele_annotator
- gain.annotation.pipeline_doc
- gain.annotation.position_score_annotator
- gain.annotation.prepare_tabular
- gain.annotation.processing_pipeline
- gain.annotation.record_to_annotatable
- gain.annotation.simple_effect_annotator
- gain.annotation.utils
- gain.annotation.value_transform_eval
- gain.binning.binners
- gain.binning.cli
- gain.binning.run_definition
- gain.dask.config
- gain.dask.named_cluster
- gain.effect_annotation.annotation_effects
- gain.effect_annotation.annotation_request
- gain.effect_annotation.annotator
- gain.effect_annotation.cli
- gain.effect_annotation.effect
- gain.effect_annotation.effect_checkers.coding
- gain.effect_annotation.effect_checkers.effect_checker
- gain.effect_annotation.effect_checkers.frame_shift
- gain.effect_annotation.effect_checkers.intron
- gain.effect_annotation.effect_checkers.promoter
- gain.effect_annotation.effect_checkers.protein_change
- gain.effect_annotation.effect_checkers.splice_site
- gain.effect_annotation.effect_checkers.start_loss
- gain.effect_annotation.effect_checkers.stop_loss
- gain.effect_annotation.effect_checkers.utr
- gain.effect_annotation.gene_codes
- gain.effect_annotation.variant
- gain.gene_scores.gene_scores
- gain.gene_scores.implementations.gene_scores_impl
- gain.gene_sets.gene_set
- gain.gene_sets.gene_term
- gain.gene_sets.implementations.gene_sets_impl
- gain.genomic_resources
- gain.genomic_resources.aggregators
- gain.genomic_resources.allele_classification
- gain.genomic_resources.ann_data_10x
- gain.genomic_resources.ann_data_resource
- gain.genomic_resources.bigwig_scores
- gain.genomic_resources.cached_repository
- gain.genomic_resources.cli
- gain.genomic_resources.cli_cache_repo
- gain.genomic_resources.cli_dvc
- gain.genomic_resources.cli_errors
- gain.genomic_resources.cli_list
- gain.genomic_resources.data_frame_resource
- gain.genomic_resources.draw_score_histograms
- gain.genomic_resources.dvc
- gain.genomic_resources.fsspec_protocol
- gain.genomic_resources.gene_models.default_attributes
- gain.genomic_resources.gene_models.gene_models
- gain.genomic_resources.gene_models.gene_models_factory
- gain.genomic_resources.gene_models.parsers
- gain.genomic_resources.gene_models.record_cells
- gain.genomic_resources.gene_models.serialization
- gain.genomic_resources.gene_models.to_gpf_gene_models_format
- gain.genomic_resources.gene_models.transcript_models
- gain.genomic_resources.genomic_context
- gain.genomic_resources.genomic_context_base
- gain.genomic_resources.genomic_context_cli
- gain.genomic_resources.genomic_position_table.index_columns
- gain.genomic_resources.genomic_position_table.line
- gain.genomic_resources.genomic_position_table.record
- gain.genomic_resources.genomic_position_table.table
- gain.genomic_resources.genomic_position_table.table_bigwig
- gain.genomic_resources.genomic_position_table.table_inmemory
- gain.genomic_resources.genomic_position_table.table_tabix
- gain.genomic_resources.genomic_position_table.table_vcf
- gain.genomic_resources.genomic_position_table.utils
- gain.genomic_resources.genomic_scores.aggregation
- gain.genomic_resources.genomic_scores.allele
- gain.genomic_resources.genomic_scores.base
- gain.genomic_resources.genomic_scores.builders
- gain.genomic_resources.genomic_scores.chrom_lengths
- gain.genomic_resources.genomic_scores.fragment
- gain.genomic_resources.genomic_scores.position
- gain.genomic_resources.genomic_scores.records
- gain.genomic_resources.genomic_scores.value_extraction
- gain.genomic_resources.group_repository
- gain.genomic_resources.histogram
- gain.genomic_resources.implementations.ann_data_resource_impl
- gain.genomic_resources.implementations.annotation_pipeline_impl
- gain.genomic_resources.implementations.basic_resource_impl
- gain.genomic_resources.implementations.data_frame_resource_impl
- gain.genomic_resources.implementations.gene_models_impl
- gain.genomic_resources.implementations.genomic_scores_impl.allele
- gain.genomic_resources.implementations.genomic_scores_impl.base
- gain.genomic_resources.implementations.genomic_scores_impl.builders
- gain.genomic_resources.implementations.genomic_scores_impl.fragment
- gain.genomic_resources.implementations.genomic_scores_impl.position
- gain.genomic_resources.implementations.genomic_scores_impl.scan
- gain.genomic_resources.implementations.liftover_chain_impl
- gain.genomic_resources.implementations.reference_genome_impl
- gain.genomic_resources.liftover_chain
- gain.genomic_resources.reference_genome
- gain.genomic_resources.repository
- gain.genomic_resources.repository_factory
- gain.genomic_resources.resource_errors
- gain.genomic_resources.resource_implementation
- gain.genomic_resources.resource_query
- gain.genomic_resources.resource_types
- gain.genomic_resources.score_def
- gain.genomic_resources.score_filter
- gain.genomic_resources.score_implementation
- gain.genomic_resources.score_resource
- gain.genomic_resources.statistics.alleles
- gain.genomic_resources.statistics.base_statistic
- gain.genomic_resources.statistics.coverage
- gain.genomic_resources.statistics.fragments
- gain.genomic_resources.statistics.indel_lengths
- gain.genomic_resources.statistics.length_histogram
- gain.genomic_resources.statistics.min_max
- gain.genomic_resources.statistics.percentages
- gain.genomic_resources.statistics.record_validation
- gain.genomic_resources.statistics.region_fold
- gain.genomic_resources.testing
- gain.genomic_resources.testing.ann_data_builder
- gain.genomic_resources.testing.builders
- gain.genomic_resources.testing.data_frame_builder
- gain.genomic_resources.testing.faulty_filesystem
- gain.genomic_resources.testing.gene_models_builder
- gain.genomic_resources.testing.group_builder
- gain.genomic_resources.testing.info_page_fixtures
- gain.genomic_resources.testing.resource_meta
- gain.genomic_resources.testing.score_specs
- gain.genomic_resources.utils
- gain.genomic_resources.variant_utils
- gain.genomic_resources.vcf_scores
- gain.task_graph.base_executor
- gain.task_graph.cache
- gain.task_graph.cli_tools
- gain.task_graph.dask_executor
- gain.task_graph.dask_run_state
- gain.task_graph.demo_graphs_cli
- gain.task_graph.executor
- gain.task_graph.graph
- gain.task_graph.logging
- gain.task_graph.process_pool_executor
- gain.task_graph.sequential_executor
- gain.task_graph.work_dir
- gain.templates
- gain.testing.acgt_import
- gain.testing.alla_import
- gain.testing.foobar_import
- gain.testing.t4c8_import
- gain.utils.chromosome_order
- gain.utils.cnv_utils
- gain.utils.dae_utils
- gain.utils.debug_closing
- gain.utils.dict_utils
- gain.utils.fs_utils
- gain.utils.helpers
- gain.utils.log_safety
- gain.utils.processing_pipeline
- gain.utils.regions
- gain.utils.resource_id_order
- gain.utils.stats_collection
- gain.utils.stringify
- gain.utils.url_redaction
- gain.utils.variant_utils
- gain.utils.verbosity_configuration