Files in Paradigm4/revealgenomics
SciDB REVEAL/Genomics API
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS-api-dev.md
R/admin-api.R
R/api2_load-api.R
R/api2_load-helper.R
R/api2_template-helper.R
R/api_choices.R
R/api_dataframe_loader.R
R/api_dataframe_reader.R
R/api_excel_loader.R
R/cache.R
R/delete.R
R/delete_featureset.R
R/entity-schema.R
R/feature-synonym.R
R/functions-feature-index.R
R/functions-gtf.R
R/functions-plot.R
R/functions-register-cached.R
R/functions-register-general.R
R/functions-register-measurementdata.R
R/functions-search-index.R
R/functions-svd.R
R/functions.R
R/functions_binary.R
R/functions_cytof.R
R/get-metadata.R
R/helper-functions.R
R/init.R
R/json-helper.R
R/measurement-statistics.R
R/measurements.R
R/package.R
R/qc_functions.R
R/r_object_in_scidb.R
R/scidb-helper-functions.R
R/search.R
R/tests-register.R
R/versioning.R
README.md
data/SCHEMA.yaml
inst/extdata/config_gff_gtf_loader.yaml
inst/extdata/data_study_a_TophatFusion_Results.txt
inst/extdata/data_study_a_signature_classification_geneset_categorical.txt
inst/extdata/data_study_a_signature_classification_geneset_continuous.txt
inst/extdata/data_study_a_variant_fusion_cnv__fmi.txt
inst/extdata/data_study_a_variant_fusion_cnv__fmi_format2.txt
inst/extdata/data_study_b_1004_L1.D443.defuse.results.filtered.tsv
inst/extdata/data_study_b_1004_L1.D443.tophat.fusions.filtered.txt
inst/extdata/data_study_b_1022_L1.D354.defuse.results.filtered.tsv
inst/extdata/data_study_b_1022_L1.D354.tophat.fusions.filtered.txt
inst/extdata/data_study_b_1058_L3.D125.tophat.fusions.filtered.txt
inst/extdata/dataloader_config.yaml
inst/extdata/datareader_config.yaml
inst/extdata/datareader_file_format_handler.yaml
inst/extdata/gene__gencode_grch38_v24__newGene.tsv.gz
inst/extdata/gene__grch38_release85_homosap_gene__newGene.tsv.gz
inst/extdata/gene__grch38_release85_homosap_gene__newTranscript.tsv.gz
inst/extdata/gene__hugo__hgnc_complete_set.txt.gz
inst/extdata/revealgenomics_config_sample.yaml
inst/extdata/rnaseq.txt
inst/extdata/scidb_metadata_sample.xlsx
inst/extdata/scidb_metadata_template.xlsx
inst/extdata/travis-manual-tests.R
man/Choices.Rd
man/DataLoader.Rd
man/DataLoaderCopyNumberVariantFormatA.Rd
man/DataLoaderVariantExomic.Rd
man/DataLoaderVariantFormatA.Rd
man/DataLoaderVariantGemini.Rd
man/DataReaderCopyNumberVariantVariableColumns.Rd
man/DataReaderVariantFormatA.Rd
man/FeaturesetChoices.Rd
man/FilterChoices.Rd
man/PipelineChoices.Rd
man/add_user_to_data_loaders.Rd
man/aggr_proj_study_by_pheno.Rd
man/api_register_biosamples.Rd
man/api_register_definitions.Rd
man/api_register_featuresets_experimentsets_measurementsets.Rd
man/api_register_individuals.Rd
man/api_register_measurements.Rd
man/api_register_ontology_from_definition_sheet.Rd
man/as.scidb_int64_cols.Rd
man/autoconvert_char.Rd
man/build_reference_gene_set.Rd
man/calculate_statistics_across_measurementsets.Rd
man/calculate_statistics_across_measurementsets_from_measurementdata_cache.Rd
man/calculate_statistics_rnaquantification.Rd
man/calculate_statistics_variant.Rd
man/check_if_revealgenomics_dataframes_equal.Rd
man/convertToExpressionSet.Rd
man/createSpectralMap.Rd
man/custom_scan.Rd
man/delete_featureset.Rd
man/download_unpivot_info_join.Rd
man/estimate_measurementdata_download_size.Rd
man/feature_matching_level1.Rd
man/filter_on_dataset_id_and_version.Rd
man/find_dataset_id_by_grep.Rd
man/find_dataset_id_by_metadata_value.Rd
man/find_matches_and_return_indices.Rd
man/find_matching_featureset.Rd
man/find_project_id_by_grep.Rd
man/flexible_mpm.Rd
man/formulate_build_literal_query.Rd
man/formulate_cell_population_data_tree_from_features_dataframe.Rd
man/formulate_feature_source_from_measuremenset.Rd
man/formulate_versioned_selection_query.Rd
man/full_arrayname.Rd
man/get_entity_from_cache.Rd
man/get_entity_from_entity_id.Rd
man/get_entity_id.Rd
man/get_entity_infoArrayExists.Rd
man/get_experiments.Rd
man/get_genelist_gene_symbols.Rd
man/get_individuals.Rd
man/get_list_of_arrays.Rd
man/get_logged_in_user.Rd
man/get_mandatory_fields_for_register_entity.Rd
man/get_measurements.Rd
man/grant_initial_access.Rd
man/init_db.Rd
man/init_r_object_cache.Rd
man/is_entity_cached.Rd
man/join_info.Rd
man/join_info_unpivot.Rd
man/lean_esetSpectralMap.Rd
man/list_datasets.Rd
man/list_ncol_in_aux_column.Rd
man/list_nrow_in_aux_column.Rd
man/list_users.Rd
man/load_helper_column_rename.Rd
man/load_helper_do_entity_specific_work.Rd
man/load_helper_handle_duplicates.Rd
man/load_helper_prepare_dataframe.Rd
man/load_helper_replace_local_ids.Rd
man/mandatory_fields.Rd
man/match_features.Rd
man/merge_aux_info_from_df.Rd
man/merge_aux_info_from_file.Rd
man/myExcelLoader.Rd
man/myExcelReader.Rd
man/na_to_blank.Rd
man/names_to_numbered_vec_by_uniqueness.Rd
man/populate_measurements.Rd
man/prep_df_fields.Rd
man/pretty_print.Rd
man/register_copynumbervariant_variable_columns.Rd
man/register_entities_excel.Rd
man/register_entities_workbook.Rd
man/register_entity_flex_fields.Rd
man/register_expression_dataframe.Rd
man/register_expression_matrix.Rd
man/register_expression_matrix_client.Rd
man/register_features_from_gtf_file.Rd
man/register_features_from_gxf_file.Rd
man/register_gene_symbol.Rd
man/register_genelist.Rd
man/register_genelist_gene.Rd
man/register_in_memory_matrix.Rd
man/register_mandatory_and_flex_fields.Rd
man/register_r_object_at_key.Rd
man/remove_old_versions_for_entity.Rd
man/remove_versions.Rd
man/retrieve_r_object_at_key.Rd
man/return_sub_indices.Rd
man/revealgenomics.Rd
man/run_quality_control_checks.Rd
man/run_tests_dataframe.Rd
man/search_copy_number_variant.Rd
man/search_copynumbervariant_variable_columns.Rd
man/search_expression.Rd
man/search_expression_by_one_measurementset_zero_or_more_features.Rd
man/search_expression_by_one_or_more_biosamples.Rd
man/search_feature_by_synonym.Rd
man/search_features.Rd
man/search_fusion.Rd
man/search_individuals.Rd
man/search_measurementdata.Rd
man/search_metadata_attrkey.Rd
man/search_metadata_value.Rd
man/search_ontology_category.Rd
man/search_rnaquantification.Rd
man/search_variant.Rd
man/search_variants.Rd
man/search_variants_scidb.Rd
man/search_versioned_secure_metadata_entity.Rd
man/search_versioned_secure_metadata_entity_by_requested_attributes.Rd
man/select_from_1d_entity.Rd
man/set_permissions.Rd
man/show_dataset_permissions.Rd
man/show_roles_for_user.Rd
man/show_user_permissions.Rd
man/template_helper_assign_experiment_entity.Rd
man/template_helper_assign_measurement_entity.Rd
man/template_helper_convert_names.Rd
man/template_helper_enforce_columns_defined.Rd
man/template_helper_enforce_mandatory_columns_present.Rd
man/template_helper_extract_definitions.Rd
man/template_helper_extract_pipeline_meta_info.Rd
man/template_helper_extract_record_related_rows.Rd
man/template_helper_formulate_file_path.Rd
man/template_helper_suffix_by_entity.Rd
man/template_linker.Rd
man/user_confirms_action.Rd
tests/run_testthat_tests.R
tests/testthat.R
tests/testthat/test-convert-dataframe-to-matrix.R
tests/testthat/test-expressionset-formation.R
tests/testthat/test00-helper-functions.R
tests/testthat/test00-schema.R
tests/testthat/test01-caching.R
tests/testthat/test02-excel_loader.R
tests/testthat/test03-register.R
tests/testthat/test04-features.R
tests/testthat/test88-gxf-loader.R
tests/testthat/test99-api-loader.R
vignettes/README.md
vignettes/setup.Rmd
