Paradigm4/revealgenomics
SciDB REVEAL/Genomics API

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462
Source code
49
Man pages
142
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Paradigm4/revealgenomics: SciDB REVEAL/Genomics API
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API

API for Paradigm4/revealgenomics
SciDB REVEAL/Genomics API

Global functions
.onAttach Source code
Choices Man page
DataLoader Man page
DataLoaderCopyNumberVariantFormatA Man page
DataLoaderVariantExomic Man page
DataLoaderVariantFormatA Man page
DataLoaderVariantGemini Man page
DataReaderCopyNumberVariantVariableColumns Man page
DataReaderVariantFormatA Man page
FeaturesetChoices Man page
FilterChoices Man page
PERMISSIONS_ARRAY Source code
PipelineChoices Man page
add_user_to_data_loaders Man page Source code
aggr_proj_study_by_pheno Man page Source code
api_register_biosamples Man page Source code
api_register_definitions Man page Source code
api_register_featuresets_experimentsets_measurementsets Man page Source code
api_register_individuals Man page Source code
api_register_measurements Man page Source code
api_register_ontology_from_definition_sheet Man page Source code
api_register_project_datasets Source code
apply_definition_constraints Source code
as.scidb_int64_cols Man page Source code
autoconvert_char Man page Source code
build_reference_gene_set Man page Source code
calculate_statistics_across_measurementsets Man page Source code
calculate_statistics_across_measurementsets_from_measurementdata Man page Source code
calculate_statistics_rnaquantification Man page Source code
calculate_statistics_variant Man page Source code
check_args_get Source code
check_args_search Source code
check_entity_exists_at_id Source code
check_if_revealgenomics_dataframes_equal Man page
combine_duplicate_column Source code
convertToExpressionSet Man page Source code
convert_attr_double_to_int64 Source code
convert_to_id_ranges Source code
count_unique_calls Source code
createDataLoader Source code
createDataReader Source code
createSpectralMap Man page Source code
cross_join_select_by_two_dims Source code
custom_scan Man page Source code
delete_dataset Source code
delete_dataset_internal Source code
delete_entity Source code
delete_featureset Man page Source code
delete_info_fields Source code
delete_project Source code
download_unpivot_info_join Man page Source code
drop_equi_join_dims Source code
entity_to_excel_sheet_converter Source code
estimate_measurementdata_download_size Man page Source code
feature_matching_level1 Man page Source code
filter_feature_df_by_cell_population Source code
filter_on_dataset_id_and_version Man page Source code
find_dataset_id_by_grep Man page Source code
find_dataset_id_by_metadata_value Man page Source code
find_entities_that_have_features Source code
find_matches_and_return_indices Man page
find_matches_with_db Source code
find_matching_featureset Man page Source code
find_namespace Source code
find_project_id_by_grep Man page Source code
flexible_mpm Man page Source code
form_selector_query_1d_array Source code
form_selector_query_secure_array Source code
formulate_base_selection_query Source code
formulate_build_literal_query Man page Source code
formulate_cell_population_data_tree_from_features_dataframe Man page Source code
formulate_equi_join_query Source code
formulate_feature_source_from_measuremenset Man page Source code
formulate_list_expression_set Source code
formulate_versioned_selection_query Man page Source code
full_arrayname Man page Source code
get_base_idname Source code
get_biosamples Source code
get_chromosome_key Source code
get_chromosome_key_from_cache Source code
get_dataset_max_version Source code
get_dataset_permissions_archive Source code
get_dataset_subelements Source code
get_dataset_version_lookup Source code
get_datasets Source code
get_definition_from_cache Source code
get_definitions Source code
get_delete_by_entity Source code
get_entity Source code
get_entity_class Source code
get_entity_data_class Source code
get_entity_from_cache Man page Source code
get_entity_from_entity_id Man page Source code
get_entity_id Man page Source code
get_entity_info Source code
get_entity_infoArrayExists Man page Source code
get_entity_names Source code
get_experiments Man page Source code
get_experimentset Source code
get_feature_synonym Source code
get_feature_synonym_from_cache Source code
get_features Source code
get_featuresets Source code
get_gene_symbol Source code
get_gene_symbol_from_cache Source code
get_genelist Source code
get_genelist_gene_symbols Man page Source code
get_idname Source code
get_individuals Man page Source code
get_infoArray Source code
get_int64fields Source code
get_list_of_arrays Man page Source code
get_logged_in_user Man page Source code
get_mandatory_fields_for_register_entity Man page Source code
get_max_id Source code
get_measurements Man page Source code
get_measurementsets Source code
get_metadata_attrkey Source code
get_metadata_attrkey_from_cache Source code
get_metadata_value Source code
get_metadata_value_from_cache Source code
get_ontology Source code
get_ontology_category Source code
get_ontology_category_from_cache Source code
get_ontology_from_cache Source code
get_projects Source code
get_referenceset Source code
get_revealgenomics_config Source code
get_search_by_entity Source code
get_variant_key Source code
get_variant_key_from_cache Source code
get_versioned_secure_metadata_entity Source code
grant_initial_access Man page Source code
handle_duplicate_name_source Source code
increment_dataset_version Source code
init_db Man page Source code
init_permissions_array Source code
init_r_object_cache Man page Source code
is_entity_cached Man page Source code
is_entity_secured Source code
is_entity_versioned Source code
join_info Man page Source code
join_info_unpivot Man page Source code
join_ontology_terms Source code
latest_version Source code
lean_esetSpectralMap Man page Source code
list_datasets Man page Source code
list_name_source_by_hierarchy Source code
list_ncol_in_aux_column Man page Source code
list_nrow_in_aux_column Man page Source code
list_users Man page Source code
load_helper_column_rename Man page Source code
load_helper_do_entity_specific_work Man page Source code
load_helper_handle_duplicates Man page Source code
load_helper_prepare_dataframe Man page Source code
load_helper_replace_local_ids Man page Source code
mandatory_fields Man page Source code
match_features Man page Source code
measurementdata_cache_download_subpart Source code
measurementdata_cache_get_download_size Source code
measurementdata_cache_get_num_subparts Source code
measurementdata_cache_is_cache_valid Source code
measurementdata_cache_return_metadata Source code
merge_aux_info_from_df Man page Source code
merge_aux_info_from_file Man page Source code
merge_gene_annotation_and_location Source code
myExcelLoader Man page Source code
myExcelReader Man page Source code
na_to_blank Man page
names_to_numbered_vec_by_uniqueness Man page
plot_heatmap_for_expression_set Source code
populate_measurements Man page Source code
prep_df_fields Man page
pretty_print Man page
print_dataset_subelements Source code
register_biosample Source code
register_chromosome_key Source code
register_copynumbervariant_variable_columns Man page Source code
register_dataset Source code
register_dataset_permissions_archive Source code
register_definitions Source code
register_entities_excel Man page Source code
register_entities_workbook Man page Source code
register_entity_flex_fields Man page Source code
register_exomic_variant Source code
register_experimentset Source code
register_expression_dataframe Man page Source code
register_expression_matrix Man page Source code
register_expression_matrix_client Man page Source code
register_feature Source code
register_feature_summary_at_measurementset Source code
register_feature_synonym Source code
register_features_from_gtf_file Man page Source code
register_features_from_gxf_file Man page Source code
register_featureset Source code
register_fusion Source code
register_gene_symbol Man page Source code
register_genelist Man page Source code
register_genelist_gene Man page Source code
register_in_memory_matrix Man page Source code
register_individual Source code
register_info Source code
register_mandatory_and_flex_fields Man page Source code
register_measurement Source code
register_measurementdata_cache Source code
register_measurementset Source code
register_metadata_attrkey Source code
register_metadata_value Source code
register_ontology_category Source code
register_ontology_term Source code
register_project Source code
register_r_object_at_key Man page Source code
register_referenceset Source code
register_tuple Source code
register_tuple_return_id Source code
register_variant Source code
register_variant_key Source code
register_versioned_secure_metadata_entity Source code
remove_old_versions_for_entity Man page Source code
remove_versions Man page Source code
report_missing_mandatory_fields Source code
retrieve_r_object_at_key Man page Source code
return_sub_indices Man page Source code
revealgenomics Man page
rg_connect Source code
rg_connect2 Source code
run_common_operations_on_search_metadata_output Source code
run_quality_control_checks Man page Source code
run_tests_dataframe Man page Source code
scidb_array_count Source code
scidb_array_head Source code
scidb_attribute_rename Source code
scidb_exists_array Source code
search_attributes Source code
search_biosamples Source code
search_copy_number_variant Man page Source code
search_copynumbervariant_variable_columns Man page Source code
search_cytof Source code
search_dataset_permissions_archive Source code
search_datasets Source code
search_definitions Source code
search_entity Source code
search_entity_flex_fields Source code
search_experimentsets Source code
search_expression Man page Source code
search_expression_by_one_measurementset_zero_or_more_features Man page Source code
search_expression_by_one_or_more_biosamples Man page Source code
search_feature_by_synonym Man page Source code
search_features Man page Source code
search_fusion Man page Source code
search_fusions_scidb Source code
search_gene_symbols Source code
search_genelist_gene Source code
search_individuals Man page Source code
search_measurementdata Man page Source code
search_measurementdata_cache Source code
search_measurements Source code
search_measurementsets Source code
search_metadata_attrkey Man page Source code
search_metadata_value Man page Source code
search_ontology_category Man page Source code
search_rnaquantification Man page Source code
search_rnaquantification_scidb Source code
search_variant Man page Source code
search_variants Man page Source code
search_variants_scidb Man page Source code
search_versioned_secure_metadata_entity Man page Source code
search_versioned_secure_metadata_entity_by_requested_attributes Man page Source code
select_from_1d_entity Man page Source code
set_permissions Man page Source code
show_dataset_permissions Man page Source code
show_permissions_inner Source code
show_roles_for_user Man page Source code
show_user_permissions Man page Source code
split_synonyms_by_pipe Source code
template_helper_assign_experiment_entity Man page Source code
template_helper_assign_measurement_entity Man page Source code
template_helper_convert_names Man page Source code
template_helper_enforce_columns_defined Man page Source code
template_helper_enforce_mandatory_columns_present Man page Source code
template_helper_extract_definitions Man page Source code
template_helper_extract_pipeline_meta_info Man page Source code
template_helper_extract_record_related_rows Man page Source code
template_helper_formulate_file_path Man page Source code
template_helper_suffix_by_entity Man page Source code
template_linker Man page
test_dataframe_formatting Source code
test_mandatory_fields Source code
test_register_biosample Source code
test_register_chromosome_key Source code
test_register_copynumbervariant_variable_columns Source code
test_register_dataset Source code
test_register_dataset_permissions_archive Source code
test_register_definition Source code
test_register_exomic_variant Source code
test_register_experimentset Source code
test_register_expression_dataframe Source code
test_register_expression_matrix Source code
test_register_feature Source code
test_register_feature_synonym Source code
test_register_featureset Source code
test_register_fusion Source code
test_register_gene_symbol Source code
test_register_genelist Source code
test_register_genelist_gene Source code
test_register_individual Source code
test_register_measurementset Source code
test_register_metadata_attrkey Source code
test_register_metadata_value Source code
test_register_ontology Source code
test_register_ontology_category Source code
test_register_project Source code
test_register_referenceset Source code
test_register_variant Source code
test_register_variant_key Source code
test_register_versioned_secure_metadata_entity Source code
test_return_carriage_in_df Source code
test_unique_fields Source code
unique_fields Source code
unpivot Source code
unpivot_key_value_pairs Source code
unpivot_variant_data Source code
update_chromosome_key_cache Source code
update_definition_cache Source code
update_entity_cache Source code
update_entity_via_excel_loader Source code
update_feature_synonym_cache Source code
update_gene_symbol_cache Source code
update_mandatory_and_info_fields Source code
update_metadata_attrkey_cache Source code
update_metadata_value_cache Source code
update_ontology_cache Source code
update_ontology_category_cache Source code
update_tuple Source code
update_variant_key_cache Source code
upload_variant_data_in_steps Source code
use_ghEnv_if_null Source code
user_confirms_action Man page
yaml_to_attr_string Source code
yaml_to_dim_str Source code
Paradigm4/revealgenomics documentation built on April 7, 2020, 2:01 a.m.

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