├── .circleci └── config.yml ├── .gitignore ├── LICENSE.txt ├── README.md ├── WDL ├── infercnv │ ├── infercnv.wdl │ ├── infercnv_test.wdl │ ├── infercnv_wdl_inputs_template.json │ └── test_data │ │ ├── gencode_v19_gene_pos_devel.txt │ │ ├── infercnv_wdl_test_inputs.json │ │ ├── oligodendroglioma_expression_downsampled.counts.matrix.txt │ │ ├── oligodendroglioma_metadata.test.txt │ │ ├── oligodendroglioma_observation_clusters.test.txt │ │ ├── oligodendroglioma_reference_clusters.test.txt │ │ └── options.json └── regev3prime │ ├── regev.scrtools.1.wdl │ ├── scp.count.27.wdl │ ├── scp.mkfastq.30.wdl │ └── single-cell-portal.cellranger_orchestra.2.wdl ├── config └── regev3prime.json ├── demo_data ├── cluster_assignments_example.txt ├── cluster_coordinates_example.txt ├── cluster_example.txt ├── coordinate_labels_example.txt ├── expression_example.txt ├── expression_matrix_example.txt ├── marker_gene_list_example.txt ├── mc_compliant_metadata_example.tsv ├── metadata_example.txt ├── spatial_example.txt └── subcluster_coordinates_example.txt ├── docker_files ├── .Rhistory ├── README.md ├── for_cell-ranger-count-2.0.2 │ └── dockerfile ├── for_scRNAseq_orchestra │ └── dockerfile ├── for_scripts │ └── dockerfile └── infercnv.dockerfile ├── requirements.txt ├── scripts ├── .coveragerc ├── Commandline.py ├── PortalFiles.py ├── PortalFilesTester.py ├── Tester.py ├── __init__.py ├── authenticate.py ├── benchmarks │ ├── README.md │ └── cellranger_orchestra_pipeline.ipynb ├── cell_ranger_to_scp.py ├── cli_parser.py ├── ideogram │ ├── __init__.py │ ├── cluster_groups.py │ ├── matrix_to_ideogram_annots.py │ └── tests │ │ ├── data │ │ ├── gencode_v19_gene_pos_truncated_sorted.txt │ │ ├── oligodendroglioma_annotations_downsampled.cluster.txt │ │ └── oligodendroglioma_expression_truncated.counts.matrix.txt │ │ └── test_matrix_to_ideogram_annots.py ├── manage_study.py ├── monitoring │ ├── README.md │ └── monitor_script.sh ├── object_conversion │ └── seurat │ │ ├── SCP2Seurat.Rmd │ │ ├── SCP2Seurat.nb.html │ │ ├── generate_SCP_files.Rmd │ │ ├── generate_SCP_files.nb.html │ │ └── seurat_scp_convenience.R ├── orchestra_methods.py ├── scp_api.py ├── scp_to_infercnv.py ├── swap_column_values.py ├── test_files │ ├── coordinates.txt │ ├── coordinates_bad_body.txt │ ├── coordinates_bad_body_2.txt │ ├── coordinates_bad_header.txt │ ├── coordinates_bad_header_duplicates.txt │ ├── coordinates_deidentifed_correct.txt │ ├── coordinates_deidentifed_precreated_correct.txt │ ├── coordinates_duplicates.txt │ ├── coordinates_mapping_correct.txt │ ├── coordinates_mapping_precreated_correct.txt │ ├── coordinates_subset_1_correct.txt │ ├── coordinates_subset_3_correct.txt │ ├── expression.txt │ ├── expression_bad_body_1.txt │ ├── expression_bad_body_2.txt │ ├── expression_bad_header.txt │ ├── expression_bad_header_2.txt │ ├── expression_deidentifed_correct.txt │ ├── expression_deidentifed_precreated_correct.txt │ ├── expression_mapping_correct.txt │ ├── expression_mapping_precreated_correct.txt │ ├── expression_n.txt │ ├── expression_subset_1_correct.txt │ ├── expression_subset_4_correct.txt │ ├── gene_list.txt │ ├── gene_list_additional_label.txt │ ├── gene_list_bad_empty_value.txt │ ├── gene_list_bad_header.txt │ ├── gene_list_bad_row_length.txt │ ├── gene_list_bad_type.txt │ ├── gene_list_minus_one.txt │ ├── gene_list_plus_one.txt │ ├── gene_sorted-test_sparse_matrix.mtx │ ├── metadata.txt │ ├── metadata_bad_body_1.txt │ ├── metadata_bad_body_2.txt │ ├── metadata_bad_header.txt │ ├── metadata_bad_header_2.txt │ ├── metadata_bad_header_dup.txt │ ├── metadata_bad_no_data.txt │ ├── metadata_bad_type.txt │ ├── metadata_bad_type_id.txt │ ├── metadata_bad_type_row_length.txt │ ├── metadata_deidentifed_correct.txt │ ├── metadata_deidentifed_precreated_correct.txt │ ├── metadata_duplicates.txt │ ├── metadata_mapping_correct.txt │ ├── metadata_mapping_precreated_correct.txt │ ├── metadata_subset_1_correct.txt │ ├── metadata_subset_2_correct.txt │ └── test_sparse_matrix.mtx ├── tests │ ├── data │ │ ├── AMC_v1.1.3.json │ │ ├── alexandria_convention_schema_2.1.0.json │ │ ├── invalid_array_v1.1.3.tsv │ │ ├── studies.json │ │ ├── study_files_post.json │ │ ├── toy_cluster.txt │ │ ├── toy_metadata.txt │ │ └── valid_array_v2.1.2.txt │ ├── gcp_mocks.py │ ├── test_manage_study.py │ ├── test_scp_api.py │ └── test_scp_to_infercnv.py └── verify_portal_file.py ├── setup.py └── site_figures ├── annotate ├── 01_Single_cell_portal_welcome.png ├── 02_Summary_page.png ├── 03_Explore_tab_menu.png ├── 04_Create_annotations.png ├── 05_Select_cells.png ├── 06_Annotations_group_name.png ├── 07_lasso.png ├── 08-label.png ├── 09_Create_annotations_button.png ├── 10_view_options.png ├── 11_select_annotation.png ├── 12_view_annotation.png ├── 13-expression-annotations.png ├── 14_profile_dropdown.png ├── 15_My_annotations.png ├── 16_My_annotations_page.png └── 17_share_study.png ├── billing-projects ├── billing-projects-add-users.png ├── billing-projects-select-create.png ├── create-billing-project.png └── select-billing-projects.png ├── cellranger_scCloud ├── cellranger_scCloud_countonly_settings.png ├── running_workflow.png ├── scCloud3Dnuclei900.png ├── settings.png ├── submission_history_actions.png ├── upload_data.png ├── upload_sampleSheet.png └── workflow_sync.png ├── create_account ├── 01_home.png ├── 02_select_account.png ├── 03_confirm_permissions.png ├── 04_profile_menu.png ├── account_creation_enter_info.png ├── account_creation_finished.png ├── account_creation_select_my_studies.png ├── account_creation_select_sign_up.png └── old │ ├── 00_home.png │ ├── 01_google_login.png │ └── 02_profile_menu.png ├── create_study ├── 00_home.png ├── 01_google_login.png ├── 01_home.png ├── 02_accept_terms_of_service.png ├── 03_add_study_name.png ├── 04_add_study_embargo.png ├── 05_add_study_embargo.png ├── 06_add_study_public.png ├── 06_add_study_workspace.png ├── 07_add_study_description.png └── 08_add_study_save.png ├── download_download_files.png ├── download_select_download.png ├── download_select_study.png ├── downloading_data ├── 00_select_study.png ├── 01_select_download_tab.png ├── 03_download_data.png ├── 04_click_for_download_command.png ├── 05_copy_download_command.png ├── download_download.png ├── download_scroll.png ├── download_select_data.png └── download_select_study.png ├── gsutil └── 02_study_details.png ├── infercnv ├── infercnv_image1.png ├── infercnv_image2.png ├── infercnv_image3.png ├── infercnv_image4.png ├── infercnv_image5.png ├── infercnv_image6.png ├── infercnv_image7.png └── infercnv_image8.png ├── managing_notifications ├── firecloud_notifications.png ├── notification_choices.png ├── portal_notifications.png └── portal_profile.png ├── metadata_convention └── upload_with_metadata_convention.png ├── metadata_file ├── mc_compliant_metadata_image_crop.jpg ├── mc_compliant_metadata_image_full.jpg ├── mc_compliant_metadata_image_full.png ├── mc_compliant_metadata_image_full.psd └── mc_compliant_metadata_image_full.sketch ├── publication_best_practices ├── create_publication_link.png └── publication_link.png ├── running_workflows ├── monitor_runs_v1.png ├── select_samples_v1.png ├── select_workflows_v1.png ├── select_workflows_v2.png ├── submit_workflow_v1.png ├── submit_workflow_v2.png └── workflows_tab_v1.png ├── search_studies ├── faceted-search.png ├── inferred-search.png ├── keyword-search.png └── search-logic.png ├── sharing_private_studies ├── 00_my_studies_btn.png ├── 01_edit_study_btn.png ├── 02_share_btn.png ├── 03_share_details.png ├── 04_show_details.png └── 05_study_details.png ├── sync_data ├── 00_add_study_btn.png ├── 01_sync_from_workspace.png ├── 01_synch_from_workspace.png ├── 02_add_study_save.png ├── 02_add_study_save_btn.png ├── 03_sync_study_btn.png ├── 03a_sync_modal.png ├── 04_sync_overview.png ├── 05_sync_cluster_info.png ├── 06_sync_cluster_completed.png ├── 07_sync_expression_info.png ├── 08_sync_gene_list_info.png ├── 09_sync_metadata_info.png ├── 10_sync_misc_info.png ├── 11_sync_data_directory.png ├── 12_sync_completed.png ├── 13_orphaned_file_info.png ├── 14_orphaned_file_update.png └── 15_orphaned_file_compelted.png ├── uploading_after_created ├── 00_exp_matrix_info.png ├── 01_exp_matrix_file.png ├── 02_exp_matrix_completed.png ├── 03_metadata_info.png ├── 04_metadata_file.png ├── 05_metadata_completed.png ├── 06_cluster_info.png ├── 07_cluster_file.png ├── 08_cluster_completed.png ├── 09_fastq_nonh_info.png ├── 10_fastq_nonh_file.png ├── 11_fastq_nonh_completed.png ├── 12_fastq_human_info.png ├── 13_gene_list_info.png ├── 14_gene_list_file.png ├── 15_gene_list_completed.png ├── 16_misc_info.png ├── 17_misc_file.png ├── 18_misc_completed.png ├── 19_study_finish.png ├── 20_study_details.png ├── 21_upload_data.png └── 22_exp_matrix_info.png ├── viewing_dotplots ├── collapse_tool_options.png ├── dot_plot_shape.png ├── dot_plot_view.png 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