genie_requests

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Active version now transferred to Sage-Bionetworks organization: https://github.com/Sage-Bionetworks/genie-project-requests

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Scripts for quick checks for GENIE

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genie_requests

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Name	Name	Last commit message	Last commit date
Latest commit hhunterzinck note before archiving Apr 14, 2022 bfad80c · Apr 14, 2022 History 230 Commits
2021-08-18_sammi_oncotree_codes	2021-08-18_sammi_oncotree_codes	initial commit	Aug 19, 2021
2021-09-03_haley_case_selection_retrospective	2021-09-03_haley_case_selection_retrospective	case selection retrospective	Sep 3, 2021
2021-09-13_haley_rca_to_rcc	2021-09-13_haley_rca_to_rcc	write and save to synapse	Sep 14, 2021
2021-09-16_haley_dfci_brca_upload_coding	2021-09-16_haley_dfci_brca_upload_coding	look at previous upload checkbox coding	Sep 16, 2021
2021-09-24_haley_redcap_exports_clean_up	2021-09-24_haley_redcap_exports_clean_up	cleaning exports folder for BPC	Sep 27, 2021
2021-07-19_mike_nsclc_2.1.R	2021-07-19_mike_nsclc_2.1.R	initial commit	Aug 19, 2021
2021-07-21_haley_nsclc_2.1_retractions.R	2021-07-21_haley_nsclc_2.1_retractions.R	initial commit	Aug 19, 2021
2021-07-22_haley_nsclc_2.1_cbio.R	2021-07-22_haley_nsclc_2.1_cbio.R	initial commit	Aug 19, 2021
2021-08-09_jessica_incomplete_rows_rcc.R	2021-08-09_jessica_incomplete_rows_rcc.R	initial commit	Aug 19, 2021
2021-08-11_mike_onboarding_sop.R	2021-08-11_mike_onboarding_sop.R	initial commit	Aug 19, 2021
2021-08-12_jessica_query_605_vicc.R	2021-08-12_jessica_query_605_vicc.R	initial commit	Aug 19, 2021
2021-08-18_xindi_msk_panc_int_values.R	2021-08-18_xindi_msk_panc_int_values.R	initial commit	Aug 19, 2021
2021-08-30_michele_bpc_map.R	2021-08-30_michele_bpc_map.R	hemonc concept list	Aug 31, 2021
2021-08-30_tom_release_11_2_wake.Rmd	2021-08-30_tom_release_11_2_wake.Rmd	rmarkdown version of check	Sep 2, 2021
2021-09-02_haley_drug_masking_validation.R	2021-09-02_haley_drug_masking_validation.R	drug masking validation for me	Sep 3, 2021
2021-09-07_alishacoll_genie_tnf_no_mutations.sql	2021-09-07_alishacoll_genie_tnf_no_mutations.sql	genie forum question on version 10 TNF	Sep 8, 2021
2021-09-07_miseksean_genie_forum_fusion_breakpoints.R	2021-09-07_miseksean_genie_forum_fusion_breakpoints.R	expore MSK fusion data comments for breakpoint info	Sep 8, 2021
2021-09-07_shawn_uhn_bladder_case_selection.R	2021-09-07_shawn_uhn_bladder_case_selection.R	uhn case selection for bladder	Sep 8, 2021
2021-09-08_hbergom_genie_forum_cna_genes.R	2021-09-08_hbergom_genie_forum_cna_genes.R	added metadata for request	Sep 9, 2021
2021-09-10_haley_unmapped_bpc_drugs.R	2021-09-10_haley_unmapped_bpc_drugs.R	extract more bpc unmapped drugs	Sep 11, 2021
2021-09-10_jocelyn_copy_file.R	2021-09-10_jocelyn_copy_file.R	request to copy file on synapse	Sep 10, 2021
2021-09-10_shawn_hemonc_brca_regimens.R	2021-09-10_shawn_hemonc_brca_regimens.R	modified closing messages	Sep 10, 2021
2021-09-14_jessica_vicc_samples.R	2021-09-14_jessica_vicc_samples.R	deleted blank lines	Sep 14, 2021
2021-09-16_haley_redcap_uncoding_nas.R	2021-09-16_haley_redcap_uncoding_nas.R	generate file of genie records for manual spot check	Sep 16, 2021
2021-09-16_shawn_nsclc_sample.R	2021-09-16_shawn_nsclc_sample.R	select random sample reproducibly	Sep 17, 2021
2021-09-20_katya_unmasked_drugs.R	2021-09-20_katya_unmasked_drugs.R	check current and previous versions of tables	Sep 21, 2021
2021-09-21_haley_ids_for_export_folder_clean_up.R	2021-09-21_haley_ids_for_export_folder_clean_up.R	fix for cohort names and all sites subfolders	Sep 22, 2021
2021-09-22_alyssa_dfci_prostate_upload.R	2021-09-22_alyssa_dfci_prostate_upload.R	examine why sample ids are NA	Sep 22, 2021
2021-09-23_diana_dfci_pt_id.R	2021-09-23_diana_dfci_pt_id.R	remove extra line	Sep 23, 2021
2021-09-28_jessica_dfci_panc_complete_col.R	2021-09-28_jessica_dfci_panc_complete_col.R	check on complete column for DFCI pancreas	Sep 28, 2021
2021-09-28_sammi_ovarian_sample_in_brca.R	2021-09-28_sammi_ovarian_sample_in_brca.R	remove ovarian sample from clinical file	Sep 28, 2021
2021-09-29_katya_pfizer_user_frq.R	2021-09-29_katya_pfizer_user_frq.R	user last activity check	Sep 30, 2021
2021-10-04_hira_msk_panc_upload.R	2021-10-04_hira_msk_panc_upload.R	check for non-numeric value	Oct 4, 2021
2021-10-04_katya_pfizer_bpc_downloads.R	2021-10-04_katya_pfizer_bpc_downloads.R	update start date and sort output	Oct 5, 2021
2021-10-04_michele_vicc_panc_upload_date_formats.R	2021-10-04_michele_vicc_panc_upload_date_formats.R	check on date time formats in site upload	Oct 4, 2021
2021-10-05_asha_dfci_panc_query_signoffs.R	2021-10-05_asha_dfci_panc_query_signoffs.R	check signoff file location	Oct 5, 2021
2021-10-05_diana_dfci_panc_upload.R	2021-10-05_diana_dfci_panc_upload.R	checked upload for text values in numeric column	Oct 6, 2021
2021-10-05_hira_panc_upload_timestamps.R	2021-10-05_hira_panc_upload_timestamps.R	chech timestamp formatting	Oct 5, 2021
2021-10-05_tom_wake.R	2021-10-05_tom_wake.R	check new file for sample ID overlap	Oct 6, 2021
2021-10-08_jessica_prostate_dd.R	2021-10-08_jessica_prostate_dd.R	check previous data dictionary	Oct 8, 2021
2021-10-12_haley_genie_team_membership.R	2021-10-12_haley_genie_team_membership.R	check user team membership	Oct 12, 2021
2021-10-13_mike_bpc_release_folder.txt	2021-10-13_mike_bpc_release_folder.txt	group bpc main genie into subfolders by series	Oct 15, 2021
2021-10-15_tom_dup_drug_prefix.R	2021-10-15_tom_dup_drug_prefix.R	checking redcap dd drug codes	Oct 15, 2021
2021-10-18_mike_drug_masking_blanket.R	2021-10-18_mike_drug_masking_blanket.R	pilot check of unmasked drug calc	Oct 18, 2021
2021-10-19_jocelyn_copy_files.R	2021-10-19_jocelyn_copy_files.R	fix variable names	Oct 19, 2021
2021-10-19_shawn_bpc_dfci_prostate_ids.R	2021-10-19_shawn_bpc_dfci_prostate_ids.R	add url to script on github	Oct 19, 2021
2021-10-20_mike_drug_masking_blanket_all_cohorts.R	2021-10-20_mike_drug_masking_blanket_all_cohorts.R	calculate percentages	Oct 21, 2021
2021-10-20_shawn_drug_masking_blanket_all_cohorts.R	2021-10-20_shawn_drug_masking_blanket_all_cohorts.R	add nsclc	Oct 21, 2021
2021-10-22_haley_permission_query_speed.R	2021-10-22_haley_permission_query_speed.R	test synapse permission querying speed with different apis	Oct 22, 2021
2021-10-26_haley_dd_vs_import.R	2021-10-26_haley_dd_vs_import.R	create ordered import template	Oct 28, 2021
2021-10-26_jocelyn_move_file.R	2021-10-26_jocelyn_move_file.R	update github url	Oct 26, 2021
2021-10-26_uhn_move_file_upload.R	2021-10-26_uhn_move_file_upload.R	move file uploaded to wrong entity	Oct 26, 2021
2021-10-28_haley_ncit_drug_coding.R	2021-10-28_haley_ncit_drug_coding.R	remove commented code	Oct 29, 2021
2021-10-28_jessica_checkbox_variables.R	2021-10-28_jessica_checkbox_variables.R	add github url	Oct 28, 2021
2021-10-28_msk_age_non_numeric.R	2021-10-28_msk_age_non_numeric.R	check non-numeric values in upload	Oct 28, 2021
2021-11-01_haley_ncit_codes.py	2021-11-01_haley_ncit_codes.py	add header comments	Nov 1, 2021
2021-11-01_haley_synapse_table_updates.R	2021-11-01_haley_synapse_table_updates.R	test functions for refreshing synapse table	Nov 3, 2021
2021-11-03_haley_silence_synapse_msg.R	2021-11-03_haley_silence_synapse_msg.R	silence synapse output to console	Nov 4, 2021
2021-11-04_tom_11.4_chop.R	2021-11-04_tom_11.4_chop.R	examine main genie upload files	Nov 4, 2021
2021-11-09_jocelyn_move_file.R	2021-11-09_jocelyn_move_file.R	new move file script	Nov 9, 2021
2021-11-10_haley_case_selection_modification_check.R	2021-11-10_haley_case_selection_modification_check.R	check case selection modifications	Nov 10, 2021
2021-11-10_sammi_missing_columns_dfci_panc.R	2021-11-10_sammi_missing_columns_dfci_panc.R	check missing values	Nov 10, 2021
2021-11-12_shawn_nsclc_phase1_samples.R	2021-11-12_shawn_nsclc_phase1_samples.R	update date range and add column already in bpc	Nov 17, 2021
2021-11-15_haley_case_list_mult_sample.R	2021-11-15_haley_case_list_mult_sample.R	check case selection lists	Nov 15, 2021
2021-11-16_shawn_bladder_uhn_eligible_cases.R	2021-11-16_shawn_bladder_uhn_eligible_cases.R	double check case selection numbers	Nov 17, 2021
2021-11-16_xindi_empty_columns.R	2021-11-16_xindi_empty_columns.R	consolidate checkbox variables	Nov 17, 2021
2021-11-19_haley_cbioportal_check.R	2021-11-19_haley_cbioportal_check.R	command line for cbio validation	Nov 22, 2021
2021-11-19_ritika_nsclc_sample_list.R	2021-11-19_ritika_nsclc_sample_list.R	update provenance description	Nov 19, 2021
2021-11-19_shawn_genie_death_int.R	2021-11-19_shawn_genie_death_int.R	explore interval and date representations	Nov 19, 2021
2021-11-29_sammi_dfci_tm_data.R	2021-11-29_sammi_dfci_tm_data.R	check for missing tm data	Nov 29, 2021
2021-12-01_michelle_dd_branching_logic.R	2021-12-01_michelle_dd_branching_logic.R	check branching logic	Dec 1, 2021
2021-12-01_ritika_missing_rx_treatment_start.R	2021-12-01_ritika_missing_rx_treatment_start.R	look at derived variable components	Dec 2, 2021
2021-12-01_tom_release_schedule.R	2021-12-01_tom_release_schedule.R	update description	Dec 1, 2021
2021-12-02_haley_synapse_config_arg.py	2021-12-02_haley_synapse_config_arg.py	synapse config as parameter	Dec 2, 2021
2021-12-03_celeste_move_upload_file.R	2021-12-03_celeste_move_upload_file.R	move file on synapse	Dec 3, 2021
2021-12-06_michele_missing_patient.R	2021-12-06_michele_missing_patient.R	check for missing patient id	Dec 7, 2021
2021-12-07_haley_migrate_qa_files.sh	2021-12-07_haley_migrate_qa_files.sh	add release reports for relevant cohorts	Dec 10, 2021
2021-12-08_xindi_variable_cross_ref.R	2021-12-08_xindi_variable_cross_ref.R	cohort specific variable cross reference	Dec 8, 2021
2021-12-13_xindi_combine_variable_synopsis.R	2021-12-13_xindi_combine_variable_synopsis.R	merge variable synopsis	Dec 14, 2021
2021-12-20_tom_mg_variant_check.R	2021-12-20_tom_mg_variant_check.R	variant check	Dec 21, 2021
2021-12-21_dfci_prostate_upload_check.R	2021-12-21_dfci_prostate_upload_check.R	check upload file	Dec 21, 2021
2021-12-23_haley_update_hemonc_ncit.R	2021-12-23_haley_update_hemonc_ncit.R	update hemonc bpc mapping	Dec 24, 2021
2021-12-23_natalie_mg_cna_file.R	2021-12-23_natalie_mg_cna_file.R	check main genie cna files	Dec 23, 2021
2021-12-29_tom_mg_checks.R	2021-12-29_tom_mg_checks.R	fix yaml valid check	Dec 30, 2021
2022-01-06_haley_mg_vital_inconsistencies.R	2022-01-06_haley_mg_vital_inconsistencies.R	vital status analysis	Jan 7, 2022
2022-01-06_haley_mg_vital_inconsistencies.Rmd	2022-01-06_haley_mg_vital_inconsistencies.Rmd	add center info	Jan 7, 2022
2022-01-06_jocelyn_copy_files.R	2022-01-06_jocelyn_copy_files.R	copy files	Jan 6, 2022
2022-01-06_natalie_assay_information.sql	2022-01-06_natalie_assay_information.sql	examine assay_information.yaml alteration types	Jan 6, 2022
2022-01-10_courtney_mg_file_mod_views.R	2022-01-10_courtney_mg_file_mod_views.R	do not add custom annotations to file views	Jan 11, 2022
2022-01-10_courtney_mg_file_mod_views.sh	2022-01-10_courtney_mg_file_mod_views.sh	do not add custom annotations to file views	Jan 11, 2022
2022-01-12_marissa_intragenic_fusions.R	2022-01-12_marissa_intragenic_fusions.R	investigate fusion comments	Jan 13, 2022
2022-01-13_michele_upload_empty_rows.R	2022-01-13_michele_upload_empty_rows.R	check for extra instance	Jan 13, 2022
2022-01-14_100k_tmb_by_site.R	2022-01-14_100k_tmb_by_site.R	use ggplot2 instead of base R plots	Jan 19, 2022
2022-01-14_100k_tmb_by_site.sh	2022-01-14_100k_tmb_by_site.sh	add plotting command line	Jan 19, 2022
2022-01-14_michele_rm_extra_instance.R	2022-01-14_michele_rm_extra_instance.R	update provenance	Jan 13, 2022
2022-01-19_ashley_nsclc_patient.R	2022-01-19_ashley_nsclc_patient.R	add print commands	Jan 19, 2022
2022-01-24_jessica_derived_vars.R	2022-01-24_jessica_derived_vars.R	explore issues with derived variable code	Jan 24, 2022
2022-01-24_jocelyn_11.6.R	2022-01-24_jocelyn_11.6.R	use file center column	Jan 24, 2022
2022-01-24_michelle_date_formats.R	2022-01-24_michelle_date_formats.R	update synapse file version	Jan 25, 2022
2022-01-24_tom_duplicated_variants.R	2022-01-24_tom_duplicated_variants.R	check 12.1-consortium duplicated variants	Jan 25, 2022
2022-01-25_tom_duplicated_variants_revised.R	2022-01-25_tom_duplicated_variants_revised.R	revise file version	Jan 26, 2022
2022-01-25_tom_remove_duplicates.R	2022-01-25_tom_remove_duplicates.R	add script github url	Jan 26, 2022
2022-01-26_marissa_upload_errors.R	2022-01-26_marissa_upload_errors.R	update maf check	Jan 26, 2022
2022-01-28_jocelyn_copy_files.R	2022-01-28_jocelyn_copy_files.R	copy files	Jan 28, 2022
2022-02-02_celeste_assay_val_update.py	2022-02-02_celeste_assay_val_update.py	replace underscore with hyphen	Feb 3, 2022
2022-02-02_celeste_seq_assay_ids.R	2022-02-02_celeste_seq_assay_ids.R	exploration of seq assay ids	Feb 3, 2022
2022-02-03_haley_bladder_tumor_marker_instrument.R	2022-02-03_haley_bladder_tumor_marker_instrument.R	check bladder uploads for tumor marker data	Feb 4, 2022
2022-02-03_haley_cbio_null_start_dates.R	2022-02-03_haley_cbio_null_start_dates.R	manually remove rows from cbio files	Feb 4, 2022
2022-02-03_haley_mg_vital_error_details.sh	2022-02-03_haley_mg_vital_error_details.sh	main genie error details	Feb 3, 2022
2022-02-03_mg_vital_error_details.R	2022-02-03_mg_vital_error_details.R	upload file with header if no errors	Feb 4, 2022
2022-02-14_brooke_cbio_panc_fixes.R	2022-02-14_brooke_cbio_panc_fixes.R	explore more files	Feb 15, 2022
2022-02-14_michele_vicc_panc_upload.R	2022-02-14_michele_vicc_panc_upload.R	compare to other data upload file	Feb 15, 2022
2022-02-15_brooke_cbio_panc_survival.R	2022-02-15_brooke_cbio_panc_survival.R	make filtering more efficient	Feb 18, 2022
2022-02-15_michele_vicc_panc_upload.R	2022-02-15_michele_vicc_panc_upload.R	check other upload issue	Feb 15, 2022
2022-02-17_mike_bpc_upload_annotations.R	2022-02-17_mike_bpc_upload_annotations.R	annotate bpc upload synapse entities	Feb 17, 2022
2022-02-18_haley_test_materialized_views.py	2022-02-18_haley_test_materialized_views.py	edit materialized view creation now in production	Mar 17, 2022
2022-02-21_cbio_metadata_files_nsclc_public.sh	2022-02-21_cbio_metadata_files_nsclc_public.sh	meta data files	Feb 21, 2022
2022-02-21_cbio_survival_nsclc.R	2022-02-21_cbio_survival_nsclc.R	explore cbio survival files	Feb 22, 2022
2022-02-21_ritika_12.2-consortium_sample_ids.R	2022-02-21_ritika_12.2-consortium_sample_ids.R	check consortium and upload release sample ids	Feb 21, 2022
2022-02-24_haley_materialized_view.R	2022-02-24_haley_materialized_view.R	edit materialized view creation now in production	Mar 17, 2022
2022-02-24_xindi_release_check.R	2022-02-24_xindi_release_check.R	initial release check	Feb 25, 2022
2022-02-25_brooke_laterality_variable.R	2022-02-25_brooke_laterality_variable.R	check laterality variable missing	Feb 25, 2022
2022-02-25_msk_drug_code.R	2022-02-25_msk_drug_code.R	check missing drug code	Feb 25, 2022
2022-02-28_dfci_prostate_upload.R	2022-02-28_dfci_prostate_upload.R	check variable values	Feb 28, 2022
2022-03-04_jocelyn_hgvsp.sql	2022-03-04_jocelyn_hgvsp.sql	main genie public 9 hvgsp question	Mar 4, 2022
2022-03-07_haley_mg_invalid_files.R	2022-03-07_haley_mg_invalid_files.R	check mg validator errors	Mar 7, 2022
2022-03-08_haley_create_phase_2_placeholders.R	2022-03-08_haley_create_phase_2_placeholders.R	add all phase 2 cohorts	Apr 14, 2022
2022-03-08_mike_bpc_upload_annotations.R	2022-03-08_mike_bpc_upload_annotations.R	add phase 2 bpc upload folders and annotations	Mar 8, 2022
2022-03-15_ashley_genie_dfci_ids.R	2022-03-15_ashley_genie_dfci_ids.R	check ids in upload	Mar 15, 2022
2022-03-15_cetin_counting_genes.R	2022-03-15_cetin_counting_genes.R	cound unique hugo symbols in bed files	Mar 15, 2022
2022-03-15_dfci_invalid_code.R	2022-03-15_dfci_invalid_code.R	check for invalid codes in dfci upload	Mar 15, 2022
2022-03-15_michele_invalid_code.R	2022-03-15_michele_invalid_code.R	read all values as characters	Mar 16, 2022
2022-03-15_michele_removed_patient.R	2022-03-15_michele_removed_patient.R	check patient id removed	Mar 15, 2022
2022-03-15_prov_sample_ids.R	2022-03-15_prov_sample_ids.R	check length of prov sample ids	Mar 15, 2022
2022-03-16_msk_bladder_upload.R	2022-03-16_msk_bladder_upload.R	check for removed patients	Mar 19, 2022
2022-03-21_haley_bpc_cbioportal_exploration.R	2022-03-21_haley_bpc_cbioportal_exploration.R	look at event type	Mar 22, 2022
2022-03-21_prov_check_clinical.R	2022-03-21_prov_check_clinical.R	checks on prov upload	Mar 21, 2022
2022-03-21_tom_check_gen_info_file.R	2022-03-21_tom_check_gen_info_file.R	check genomic information file	Mar 22, 2022
2022-03-22_jessica_check_redaction.R	2022-03-22_jessica_check_redaction.R	check redaction	Mar 22, 2022
2022-03-22_tom_check_prov.R	2022-03-22_tom_check_prov.R	check prov ids across files	Mar 22, 2022
2022-03-28_cetin_wake_clinical_file.R	2022-03-28_cetin_wake_clinical_file.R	check wake upload issues	Mar 28, 2022
2022-03-28_haley_sor_data_elements_catalog.R	2022-03-28_haley_sor_data_elements_catalog.R	explore data element and sor inconsistencies	Mar 29, 2022
2022-03-30_haley_copy_folder_plus_contents.R	2022-03-30_haley_copy_folder_plus_contents.R	clean copy of folder and file contents	Mar 30, 2022
2022-04-06_stats_retract_redacted_samples.R	2022-04-06_stats_retract_redacted_samples.R	get all nsclc redacted patients	Apr 7, 2022
2022-04-07_haley_chop_mg_check.R	2022-04-07_haley_chop_mg_check.R	check missing assay ids for sites	Apr 7, 2022
2022-04-07_haley_grcc_mg_check.R	2022-04-07_haley_grcc_mg_check.R	check missing assay ids for sites	Apr 7, 2022
2022-04-07_haley_sci_mg_check.R	2022-04-07_haley_sci_mg_check.R	check prov versus sci patient ids	Apr 7, 2022
2022-04-07_haley_vicc_mg_check.R	2022-04-07_haley_vicc_mg_check.R	check missing assay ids for sites	Apr 7, 2022
2022-04-12_michelle_mg_file_errors.R	2022-04-12_michelle_mg_file_errors.R	check duke files	Apr 12, 2022
2022-04-12_susana_mg_invalid_files.R	2022-04-12_susana_mg_invalid_files.R	check vhio invalid files	Apr 12, 2022
2022-04-13_shirin_prostate_upload.R	2022-04-13_shirin_prostate_upload.R	check record id	Apr 13, 2022
LICENSE	LICENSE	add license	Apr 1, 2022
README.md	README.md	note before archiving	Apr 14, 2022
save_to_synapse.R	save_to_synapse.R	scripts to automate saving to synapse	Sep 2, 2021

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