From c00965a3deb7e3717df09ab10e3815aa5c3a6787 Mon Sep 17 00:00:00 2001 From: Alexandros Sigaras Date: Mon, 21 Mar 2022 08:16:46 -0400 Subject: [PATCH 1/5] new study: ccrcc_wcm_2022 --- public/ccrcc_wcm_2022/case_lists/cases_sequenced.txt | 5 +++++ public/ccrcc_wcm_2022/data_clinical_patient.txt | 3 +++ public/ccrcc_wcm_2022/data_clinical_sample.txt | 3 +++ public/ccrcc_wcm_2022/data_cna_hg19.seg | 3 +++ public/ccrcc_wcm_2022/data_log2_cna.txt | 3 +++ public/ccrcc_wcm_2022/data_mutations.txt | 3 +++ public/ccrcc_wcm_2022/meta_clinical_patient.txt | 4 ++++ public/ccrcc_wcm_2022/meta_clinical_sample.txt | 4 ++++ public/ccrcc_wcm_2022/meta_cna_hg19_seg.txt | 6 ++++++ public/ccrcc_wcm_2022/meta_log2_cna.txt | 8 ++++++++ public/ccrcc_wcm_2022/meta_mutation_extended.txt | 8 ++++++++ public/ccrcc_wcm_2022/meta_study.txt | 7 +++++++ 12 files changed, 57 insertions(+) create mode 100644 public/ccrcc_wcm_2022/case_lists/cases_sequenced.txt create mode 100644 public/ccrcc_wcm_2022/data_clinical_patient.txt create mode 100644 public/ccrcc_wcm_2022/data_clinical_sample.txt create mode 100644 public/ccrcc_wcm_2022/data_cna_hg19.seg create mode 100644 public/ccrcc_wcm_2022/data_log2_cna.txt create mode 100644 public/ccrcc_wcm_2022/data_mutations.txt create mode 100644 public/ccrcc_wcm_2022/meta_clinical_patient.txt create mode 100644 public/ccrcc_wcm_2022/meta_clinical_sample.txt create mode 100644 public/ccrcc_wcm_2022/meta_cna_hg19_seg.txt create mode 100644 public/ccrcc_wcm_2022/meta_log2_cna.txt create mode 100644 public/ccrcc_wcm_2022/meta_mutation_extended.txt create mode 100644 public/ccrcc_wcm_2022/meta_study.txt diff --git a/public/ccrcc_wcm_2022/case_lists/cases_sequenced.txt b/public/ccrcc_wcm_2022/case_lists/cases_sequenced.txt new file mode 100644 index 0000000000..206459225c --- /dev/null +++ b/public/ccrcc_wcm_2022/case_lists/cases_sequenced.txt @@ -0,0 +1,5 @@ +cancer_study_identifier: ccrcc_wcm_2022 +stable_id: ccrcc_wcm_2022_sequenced +case_list_name: All Sequenced data +case_list_description: All Sequenced data +case_list_ids: WCMC-RCC-036-1 WCMC-RCC-085-1 WCMC-RCC-084-1 WCMC-RCC-084-2 WCMC-RCC-081-1 WCMC-RCC-078-1 WCMC-RCC-077-1 WCMC-RCC-074-1 WCMC-RCC-074-2 WCMC-RCC-069-1 WCMC-RCC-065-1 WCMC-RCC-065-2 WCMC-RCC-060-1 WCMC-RCC-058-1 WCMC-RCC-058-2 WCMC-RCC-057-1 WCMC-RCC-051-1 WCMC-RCC-050-1 WCMC-RCC-050-2 WCMC-RCC-048-1 WCMC-RCC-048-2 WCMC-RCC-047-1 WCMC-RCC-045-1 WCMC-RCC-044-1 WCMC-RCC-043-1 WCMC-RCC-041-1 WCMC-RCC-039-1 WCMC-RCC-036-2 WCMC-RCC-035-1 WCMC-RCC-034-1 WCMC-RCC-033-1 WCMC-RCC-033-2 WCMC-RCC-032-1 WCMC-RCC-030-1 WCMC-RCC-030-2 WCMC-RCC-029-1 WCMC-RCC-029-2 WCMC-RCC-026-1 WCMC-RCC-024-1 WCMC-RCC-023-1 WCMC-RCC-022-1 WCMC-RCC-008-1 WCMC-RCC-008-2 WCMC-RCC-008-3 WCMC-RCC-008-4 WCMC-RCC-019-1 WCMC-RCC-015-1 WCMC-RCC-015-2 WCMC-RCC-015-3 WCMC-RCC-015-4 WCMC-RCC-014-1 WCMC-RCC-013-1 WCMC-RCC-007-1 WCMC-RCC-007-2 WCMC-RCC-007-3 WCMC-RCC-007-4 WCMC-RCC-007-5 WCMC-RCC-007-6 WCMC-RCC-007-7 WCMC-RCC-086-1 WCMC-RCC-010-1 WCMC-RCC-006-1 WCMC-RCC-006-2 WCMC-RCC-006-3 WCMC-RCC-003-1 WCMC-RCC-002-1 WCMC-RCC-001-1 \ No newline at end of file diff --git a/public/ccrcc_wcm_2022/data_clinical_patient.txt b/public/ccrcc_wcm_2022/data_clinical_patient.txt new file mode 100644 index 0000000000..b35c58c38d --- /dev/null +++ b/public/ccrcc_wcm_2022/data_clinical_patient.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:cf0a454e8babbea70b10da2731f58ab18e39f6d490f74ce1642059de188515f0 +size 1633 diff --git a/public/ccrcc_wcm_2022/data_clinical_sample.txt b/public/ccrcc_wcm_2022/data_clinical_sample.txt new file mode 100644 index 0000000000..e6e3a3db08 --- /dev/null +++ b/public/ccrcc_wcm_2022/data_clinical_sample.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:035ec987f650bc077ae19c21faec37acbdfd192b686bda5852ac3d03547b6835 +size 4773 diff --git a/public/ccrcc_wcm_2022/data_cna_hg19.seg b/public/ccrcc_wcm_2022/data_cna_hg19.seg new file mode 100644 index 0000000000..0bbc7b37e6 --- /dev/null +++ b/public/ccrcc_wcm_2022/data_cna_hg19.seg @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:308f8542042f32405fcb3f72806afb5dae3ae20aa02970a0c0861f6e9f5e789f +size 281793 diff --git a/public/ccrcc_wcm_2022/data_log2_cna.txt b/public/ccrcc_wcm_2022/data_log2_cna.txt new file mode 100644 index 0000000000..1da70e6ab1 --- /dev/null +++ b/public/ccrcc_wcm_2022/data_log2_cna.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:84e8fd41bfe2b24e44e8f85470dbde6d7deb1cb7fabd6ca4942e3024a8f339e8 +size 16025208 diff --git a/public/ccrcc_wcm_2022/data_mutations.txt b/public/ccrcc_wcm_2022/data_mutations.txt new file mode 100644 index 0000000000..e3d256ad4c --- /dev/null +++ b/public/ccrcc_wcm_2022/data_mutations.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:7685cc040ab84fa1718cfe06ef6aa9910aef38da6d1d1829d393ebaf7b54ddba +size 9302041 diff --git a/public/ccrcc_wcm_2022/meta_clinical_patient.txt b/public/ccrcc_wcm_2022/meta_clinical_patient.txt new file mode 100644 index 0000000000..d954c87020 --- /dev/null +++ b/public/ccrcc_wcm_2022/meta_clinical_patient.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: ccrcc_wcm_2022 +genetic_alteration_type: CLINICAL +datatype: PATIENT_ATTRIBUTES +data_filename: data_clinical_patient.txt diff --git a/public/ccrcc_wcm_2022/meta_clinical_sample.txt b/public/ccrcc_wcm_2022/meta_clinical_sample.txt new file mode 100644 index 0000000000..6d72e0c435 --- /dev/null +++ b/public/ccrcc_wcm_2022/meta_clinical_sample.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: ccrcc_wcm_2022 +genetic_alteration_type: CLINICAL +datatype: SAMPLE_ATTRIBUTES +data_filename: data_clinical_sample.txt diff --git a/public/ccrcc_wcm_2022/meta_cna_hg19_seg.txt b/public/ccrcc_wcm_2022/meta_cna_hg19_seg.txt new file mode 100644 index 0000000000..5ad18e0f23 --- /dev/null +++ b/public/ccrcc_wcm_2022/meta_cna_hg19_seg.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: ccrcc_wcm_2022 +genetic_alteration_type: COPY_NUMBER_ALTERATION +datatype: SEG +reference_genome_id: hg19 +description: Somatic CNA data(copy number ratio from tumor samples minus ratio from matched normals). +data_filename: data_cna_hg19.seg diff --git a/public/ccrcc_wcm_2022/meta_log2_cna.txt b/public/ccrcc_wcm_2022/meta_log2_cna.txt new file mode 100644 index 0000000000..f52e60145d --- /dev/null +++ b/public/ccrcc_wcm_2022/meta_log2_cna.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: ccrcc_wcm_2022 +genetic_alteration_type: COPY_NUMBER_ALTERATION +datatype: LOG2-VALUE +stable_id: log2CNA +show_profile_in_analysis_tab: false +profile_name: Log2 copy-number values for each gene. +profile_description: Log2 copy-number values +data_filename: data_log2_cna.txt diff --git a/public/ccrcc_wcm_2022/meta_mutation_extended.txt b/public/ccrcc_wcm_2022/meta_mutation_extended.txt new file mode 100644 index 0000000000..e38353bd5c --- /dev/null +++ b/public/ccrcc_wcm_2022/meta_mutation_extended.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: ccrcc_wcm_2022 +genetic_alteration_type: MUTATION_EXTENDED +datatype: MAF +stable_id: mutations +show_profile_in_analysis_tab: true +profile_description: Mutations +profile_name: Mutation data from whole exome sequencing. +data_filename: data_mutations.txt diff --git a/public/ccrcc_wcm_2022/meta_study.txt b/public/ccrcc_wcm_2022/meta_study.txt new file mode 100644 index 0000000000..a07def6994 --- /dev/null +++ b/public/ccrcc_wcm_2022/meta_study.txt @@ -0,0 +1,7 @@ +type_of_cancer: ccrcc +cancer_study_identifier: ccrcc_wcm_2022 +name: Clear Cell Renal Cell Carcinoma (Cornell, Molecular Oncology 2022) +description: Whole-exome sequencing of metastatic clear cell renal carcinoma (ccRCC) from 67 tumor/normal pairs from 43 patients. +citation: van der Mijn et al. Mol Oncol. 2022 +pmid: 35231161 +add_global_case_list: true From 0851814c5bd14d59018c25800a477630c35d8dc0 Mon Sep 17 00:00:00 2001 From: Alexandros Sigaras Date: Mon, 21 Mar 2022 08:19:53 -0400 Subject: [PATCH 2/5] updated groups to PUBLIC --- public/ccrcc_wcm_2022/meta_study.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/public/ccrcc_wcm_2022/meta_study.txt b/public/ccrcc_wcm_2022/meta_study.txt index a07def6994..e53d90d4a4 100644 --- a/public/ccrcc_wcm_2022/meta_study.txt +++ b/public/ccrcc_wcm_2022/meta_study.txt @@ -5,3 +5,4 @@ description: Whole-exome sequencing of metastatic clear cell renal carcinoma (cc citation: van der Mijn et al. Mol Oncol. 2022 pmid: 35231161 add_global_case_list: true +groups: PUBLIC From e98c9b7254a1336872e8ed1370cd90a600cccc97 Mon Sep 17 00:00:00 2001 From: Alexandros Sigaras Date: Thu, 7 Apr 2022 17:32:45 -0400 Subject: [PATCH 3/5] Updated cohort based on feedback in PR --- public/ccrcc_wcm_2022/case_lists/cases_cna.txt | 6 ++++++ public/ccrcc_wcm_2022/case_lists/cases_cnaseq.txt | 6 ++++++ public/ccrcc_wcm_2022/case_lists/cases_sequenced.txt | 5 +++-- public/ccrcc_wcm_2022/data_clinical_sample.txt | 4 ++-- .../{meta_mutation_extended.txt => meta_mutations.txt} | 0 public/ccrcc_wcm_2022/meta_study.txt | 2 +- 6 files changed, 18 insertions(+), 5 deletions(-) create mode 100644 public/ccrcc_wcm_2022/case_lists/cases_cna.txt create mode 100644 public/ccrcc_wcm_2022/case_lists/cases_cnaseq.txt rename public/ccrcc_wcm_2022/{meta_mutation_extended.txt => meta_mutations.txt} (100%) diff --git a/public/ccrcc_wcm_2022/case_lists/cases_cna.txt b/public/ccrcc_wcm_2022/case_lists/cases_cna.txt new file mode 100644 index 0000000000..697e491566 --- /dev/null +++ b/public/ccrcc_wcm_2022/case_lists/cases_cna.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: ccrcc_wcm_2022 +stable_id: ccrcc_wcm_2022_cna +case_list_name: Samples with CNA data +case_list_description: Samples with mutation data (67 tumor/normal pair samples) +case_list_category: all_cases_with_cna_data +case_list_ids: WCMC-RCC-036-1 WCMC-RCC-085-1 WCMC-RCC-084-1 WCMC-RCC-084-2 WCMC-RCC-081-1 WCMC-RCC-078-1 WCMC-RCC-077-1 WCMC-RCC-074-1 WCMC-RCC-074-2 WCMC-RCC-069-1 WCMC-RCC-065-1 WCMC-RCC-065-2 WCMC-RCC-060-1 WCMC-RCC-058-1 WCMC-RCC-058-2 WCMC-RCC-057-1 WCMC-RCC-051-1 WCMC-RCC-050-1 WCMC-RCC-050-2 WCMC-RCC-048-1 WCMC-RCC-048-2 WCMC-RCC-047-1 WCMC-RCC-045-1 WCMC-RCC-044-1 WCMC-RCC-043-1 WCMC-RCC-041-1 WCMC-RCC-039-1 WCMC-RCC-036-2 WCMC-RCC-035-1 WCMC-RCC-034-1 WCMC-RCC-033-1 WCMC-RCC-033-2 WCMC-RCC-032-1 WCMC-RCC-030-1 WCMC-RCC-030-2 WCMC-RCC-029-1 WCMC-RCC-029-2 WCMC-RCC-026-1 WCMC-RCC-024-1 WCMC-RCC-023-1 WCMC-RCC-022-1 WCMC-RCC-008-1 WCMC-RCC-008-2 WCMC-RCC-008-3 WCMC-RCC-008-4 WCMC-RCC-019-1 WCMC-RCC-015-1 WCMC-RCC-015-2 WCMC-RCC-015-3 WCMC-RCC-015-4 WCMC-RCC-014-1 WCMC-RCC-013-1 WCMC-RCC-007-1 WCMC-RCC-007-2 WCMC-RCC-007-3 WCMC-RCC-007-4 WCMC-RCC-007-5 WCMC-RCC-007-6 WCMC-RCC-007-7 WCMC-RCC-086-1 WCMC-RCC-010-1 WCMC-RCC-006-1 WCMC-RCC-006-2 WCMC-RCC-006-3 WCMC-RCC-003-1 WCMC-RCC-002-1 WCMC-RCC-001-1 \ No newline at end of file diff --git a/public/ccrcc_wcm_2022/case_lists/cases_cnaseq.txt b/public/ccrcc_wcm_2022/case_lists/cases_cnaseq.txt new file mode 100644 index 0000000000..85632fc63f --- /dev/null +++ b/public/ccrcc_wcm_2022/case_lists/cases_cnaseq.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: ccrcc_wcm_2022 +stable_id: ccrcc_wcm_2022_cnaseq +case_list_name: Samples with mutation and CNA data +case_list_description: Samples with mutation and CNA data (67 tumor/normal pair samples) +case_list_category: all_cases_with_mutation_and_cna_data +case_list_ids: WCMC-RCC-036-1 WCMC-RCC-085-1 WCMC-RCC-084-1 WCMC-RCC-084-2 WCMC-RCC-081-1 WCMC-RCC-078-1 WCMC-RCC-077-1 WCMC-RCC-074-1 WCMC-RCC-074-2 WCMC-RCC-069-1 WCMC-RCC-065-1 WCMC-RCC-065-2 WCMC-RCC-060-1 WCMC-RCC-058-1 WCMC-RCC-058-2 WCMC-RCC-057-1 WCMC-RCC-051-1 WCMC-RCC-050-1 WCMC-RCC-050-2 WCMC-RCC-048-1 WCMC-RCC-048-2 WCMC-RCC-047-1 WCMC-RCC-045-1 WCMC-RCC-044-1 WCMC-RCC-043-1 WCMC-RCC-041-1 WCMC-RCC-039-1 WCMC-RCC-036-2 WCMC-RCC-035-1 WCMC-RCC-034-1 WCMC-RCC-033-1 WCMC-RCC-033-2 WCMC-RCC-032-1 WCMC-RCC-030-1 WCMC-RCC-030-2 WCMC-RCC-029-1 WCMC-RCC-029-2 WCMC-RCC-026-1 WCMC-RCC-024-1 WCMC-RCC-023-1 WCMC-RCC-022-1 WCMC-RCC-008-1 WCMC-RCC-008-2 WCMC-RCC-008-3 WCMC-RCC-008-4 WCMC-RCC-019-1 WCMC-RCC-015-1 WCMC-RCC-015-2 WCMC-RCC-015-3 WCMC-RCC-015-4 WCMC-RCC-014-1 WCMC-RCC-013-1 WCMC-RCC-007-1 WCMC-RCC-007-2 WCMC-RCC-007-3 WCMC-RCC-007-4 WCMC-RCC-007-5 WCMC-RCC-007-6 WCMC-RCC-007-7 WCMC-RCC-086-1 WCMC-RCC-010-1 WCMC-RCC-006-1 WCMC-RCC-006-2 WCMC-RCC-006-3 WCMC-RCC-003-1 WCMC-RCC-002-1 WCMC-RCC-001-1 \ No newline at end of file diff --git a/public/ccrcc_wcm_2022/case_lists/cases_sequenced.txt b/public/ccrcc_wcm_2022/case_lists/cases_sequenced.txt index 206459225c..229ef56f95 100644 --- a/public/ccrcc_wcm_2022/case_lists/cases_sequenced.txt +++ b/public/ccrcc_wcm_2022/case_lists/cases_sequenced.txt @@ -1,5 +1,6 @@ cancer_study_identifier: ccrcc_wcm_2022 stable_id: ccrcc_wcm_2022_sequenced -case_list_name: All Sequenced data -case_list_description: All Sequenced data +case_list_name: Samples with mutation data +case_list_description: Samples with mutation data (67 tumor/normal pair samples) +case_list_category: all_cases_with_mutation_data case_list_ids: WCMC-RCC-036-1 WCMC-RCC-085-1 WCMC-RCC-084-1 WCMC-RCC-084-2 WCMC-RCC-081-1 WCMC-RCC-078-1 WCMC-RCC-077-1 WCMC-RCC-074-1 WCMC-RCC-074-2 WCMC-RCC-069-1 WCMC-RCC-065-1 WCMC-RCC-065-2 WCMC-RCC-060-1 WCMC-RCC-058-1 WCMC-RCC-058-2 WCMC-RCC-057-1 WCMC-RCC-051-1 WCMC-RCC-050-1 WCMC-RCC-050-2 WCMC-RCC-048-1 WCMC-RCC-048-2 WCMC-RCC-047-1 WCMC-RCC-045-1 WCMC-RCC-044-1 WCMC-RCC-043-1 WCMC-RCC-041-1 WCMC-RCC-039-1 WCMC-RCC-036-2 WCMC-RCC-035-1 WCMC-RCC-034-1 WCMC-RCC-033-1 WCMC-RCC-033-2 WCMC-RCC-032-1 WCMC-RCC-030-1 WCMC-RCC-030-2 WCMC-RCC-029-1 WCMC-RCC-029-2 WCMC-RCC-026-1 WCMC-RCC-024-1 WCMC-RCC-023-1 WCMC-RCC-022-1 WCMC-RCC-008-1 WCMC-RCC-008-2 WCMC-RCC-008-3 WCMC-RCC-008-4 WCMC-RCC-019-1 WCMC-RCC-015-1 WCMC-RCC-015-2 WCMC-RCC-015-3 WCMC-RCC-015-4 WCMC-RCC-014-1 WCMC-RCC-013-1 WCMC-RCC-007-1 WCMC-RCC-007-2 WCMC-RCC-007-3 WCMC-RCC-007-4 WCMC-RCC-007-5 WCMC-RCC-007-6 WCMC-RCC-007-7 WCMC-RCC-086-1 WCMC-RCC-010-1 WCMC-RCC-006-1 WCMC-RCC-006-2 WCMC-RCC-006-3 WCMC-RCC-003-1 WCMC-RCC-002-1 WCMC-RCC-001-1 \ No newline at end of file diff --git a/public/ccrcc_wcm_2022/data_clinical_sample.txt b/public/ccrcc_wcm_2022/data_clinical_sample.txt index e6e3a3db08..e0542a999e 100644 --- a/public/ccrcc_wcm_2022/data_clinical_sample.txt +++ b/public/ccrcc_wcm_2022/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:035ec987f650bc077ae19c21faec37acbdfd192b686bda5852ac3d03547b6835 -size 4773 +oid sha256:6694e8c658ca37707e7c19b33a1cfa97a05bf9cff84f86dec89b096c905d4f10 +size 9220 diff --git a/public/ccrcc_wcm_2022/meta_mutation_extended.txt b/public/ccrcc_wcm_2022/meta_mutations.txt similarity index 100% rename from public/ccrcc_wcm_2022/meta_mutation_extended.txt rename to public/ccrcc_wcm_2022/meta_mutations.txt diff --git a/public/ccrcc_wcm_2022/meta_study.txt b/public/ccrcc_wcm_2022/meta_study.txt index e53d90d4a4..70a86baa0e 100644 --- a/public/ccrcc_wcm_2022/meta_study.txt +++ b/public/ccrcc_wcm_2022/meta_study.txt @@ -1,7 +1,7 @@ type_of_cancer: ccrcc cancer_study_identifier: ccrcc_wcm_2022 name: Clear Cell Renal Cell Carcinoma (Cornell, Molecular Oncology 2022) -description: Whole-exome sequencing of metastatic clear cell renal carcinoma (ccRCC) from 67 tumor/normal pairs from 43 patients. +description: Whole-exome sequencing of metastatic clear cell renal carcinoma (ccRCC) from 67 tumor/normal pairs from 43 patients. Please note that one sample has been excluded from the original cohort as it didn't meet the quality threshold for Somatic Copy Number Analysis (SCNA). citation: van der Mijn et al. Mol Oncol. 2022 pmid: 35231161 add_global_case_list: true From 4c9856e577061e4615df10145748678ee1c13bf9 Mon Sep 17 00:00:00 2001 From: RAlhamad Date: Sun, 20 Aug 2023 22:06:19 -0400 Subject: [PATCH 4/5] Adding new public study. --- public/ccrcc_wcm_2022/case_lists/cases_all.txt | 6 ++++++ public/ccrcc_wcm_2022/case_lists/cases_log2CNA.txt | 6 ++++++ public/ccrcc_wcm_2022/case_lists/cases_sequenced.txt | 4 ++-- public/ccrcc_wcm_2022/data_mutations.txt | 4 ++-- 4 files changed, 16 insertions(+), 4 deletions(-) create mode 100644 public/ccrcc_wcm_2022/case_lists/cases_all.txt create mode 100644 public/ccrcc_wcm_2022/case_lists/cases_log2CNA.txt diff --git a/public/ccrcc_wcm_2022/case_lists/cases_all.txt b/public/ccrcc_wcm_2022/case_lists/cases_all.txt new file mode 100644 index 0000000000..15718fdfc6 --- /dev/null +++ b/public/ccrcc_wcm_2022/case_lists/cases_all.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: ccrcc_wcm_2022 +stable_id: ccrcc_wcm_2022_all +case_list_name: All samples +case_list_description: All samples (67 samples) +case_list_category: all_cases_in_study +case_list_ids: WCMC-RCC-036-1 WCMC-RCC-036-2 WCMC-RCC-084-2 WCMC-RCC-048-1 WCMC-RCC-035-1 WCMC-RCC-014-1 WCMC-RCC-057-1 WCMC-RCC-078-1 WCMC-RCC-045-1 WCMC-RCC-060-1 WCMC-RCC-043-1 WCMC-RCC-034-1 WCMC-RCC-032-1 WCMC-RCC-001-1 WCMC-RCC-033-1 WCMC-RCC-058-1 WCMC-RCC-058-2 WCMC-RCC-033-2 WCMC-RCC-015-1 WCMC-RCC-007-1 WCMC-RCC-007-2 WCMC-RCC-015-2 WCMC-RCC-007-4 WCMC-RCC-007-5 WCMC-RCC-006-3 WCMC-RCC-007-7 WCMC-RCC-006-1 WCMC-RCC-069-1 WCMC-RCC-007-6 WCMC-RCC-008-4 WCMC-RCC-008-3 WCMC-RCC-008-2 WCMC-RCC-008-1 WCMC-RCC-022-1 WCMC-RCC-081-1 WCMC-RCC-086-1 WCMC-RCC-023-1 WCMC-RCC-015-3 WCMC-RCC-010-1 WCMC-RCC-013-1 WCMC-RCC-041-1 WCMC-RCC-048-2 WCMC-RCC-084-1 WCMC-RCC-050-1 WCMC-RCC-050-2 WCMC-RCC-051-1 WCMC-RCC-085-1 WCMC-RCC-047-1 WCMC-RCC-065-1 WCMC-RCC-065-2 WCMC-RCC-030-2 WCMC-RCC-044-1 WCMC-RCC-030-1 WCMC-RCC-019-1 WCMC-RCC-029-1 WCMC-RCC-029-2 WCMC-RCC-015-4 WCMC-RCC-024-1 WCMC-RCC-026-1 WCMC-RCC-006-2 WCMC-RCC-077-1 WCMC-RCC-003-1 WCMC-RCC-002-1 WCMC-RCC-007-3 WCMC-RCC-039-1 WCMC-RCC-074-2 WCMC-RCC-074-1 diff --git a/public/ccrcc_wcm_2022/case_lists/cases_log2CNA.txt b/public/ccrcc_wcm_2022/case_lists/cases_log2CNA.txt new file mode 100644 index 0000000000..54766b9d6c --- /dev/null +++ b/public/ccrcc_wcm_2022/case_lists/cases_log2CNA.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: ccrcc_wcm_2022 +stable_id: ccrcc_wcm_2022_log2CNA +case_list_name: Samples with log2 copy-number data +case_list_description: Samples with log2 copy-number data (67 samples) +case_list_category: all_cases_with_log2_cna_data +case_list_ids: WCMC-RCC-084-2 WCMC-RCC-084-1 WCMC-RCC-036-1 WCMC-RCC-036-2 WCMC-RCC-048-2 WCMC-RCC-051-1 WCMC-RCC-033-1 WCMC-RCC-015-3 WCMC-RCC-048-1 WCMC-RCC-035-1 WCMC-RCC-058-1 WCMC-RCC-057-1 WCMC-RCC-078-1 WCMC-RCC-085-1 WCMC-RCC-045-1 WCMC-RCC-047-1 WCMC-RCC-050-1 WCMC-RCC-060-1 WCMC-RCC-065-1 WCMC-RCC-065-2 WCMC-RCC-034-1 WCMC-RCC-030-2 WCMC-RCC-050-2 WCMC-RCC-044-1 WCMC-RCC-007-1 WCMC-RCC-032-1 WCMC-RCC-001-1 WCMC-RCC-019-1 WCMC-RCC-014-1 WCMC-RCC-058-2 WCMC-RCC-033-2 WCMC-RCC-015-1 WCMC-RCC-029-1 WCMC-RCC-007-2 WCMC-RCC-015-2 WCMC-RCC-006-1 WCMC-RCC-069-1 WCMC-RCC-006-3 WCMC-RCC-006-2 WCMC-RCC-007-4 WCMC-RCC-007-5 WCMC-RCC-007-6 WCMC-RCC-043-1 WCMC-RCC-024-1 WCMC-RCC-008-4 WCMC-RCC-008-3 WCMC-RCC-008-2 WCMC-RCC-008-1 WCMC-RCC-022-1 WCMC-RCC-081-1 WCMC-RCC-026-1 WCMC-RCC-010-1 WCMC-RCC-086-1 WCMC-RCC-013-1 WCMC-RCC-015-4 WCMC-RCC-077-1 WCMC-RCC-023-1 WCMC-RCC-007-7 WCMC-RCC-030-1 WCMC-RCC-003-1 WCMC-RCC-002-1 WCMC-RCC-007-3 WCMC-RCC-029-2 WCMC-RCC-039-1 WCMC-RCC-041-1 WCMC-RCC-074-2 WCMC-RCC-074-1 diff --git a/public/ccrcc_wcm_2022/case_lists/cases_sequenced.txt b/public/ccrcc_wcm_2022/case_lists/cases_sequenced.txt index 229ef56f95..37f1e79807 100644 --- a/public/ccrcc_wcm_2022/case_lists/cases_sequenced.txt +++ b/public/ccrcc_wcm_2022/case_lists/cases_sequenced.txt @@ -1,6 +1,6 @@ cancer_study_identifier: ccrcc_wcm_2022 stable_id: ccrcc_wcm_2022_sequenced case_list_name: Samples with mutation data -case_list_description: Samples with mutation data (67 tumor/normal pair samples) +case_list_description: Samples with mutation data (67 samples) case_list_category: all_cases_with_mutation_data -case_list_ids: WCMC-RCC-036-1 WCMC-RCC-085-1 WCMC-RCC-084-1 WCMC-RCC-084-2 WCMC-RCC-081-1 WCMC-RCC-078-1 WCMC-RCC-077-1 WCMC-RCC-074-1 WCMC-RCC-074-2 WCMC-RCC-069-1 WCMC-RCC-065-1 WCMC-RCC-065-2 WCMC-RCC-060-1 WCMC-RCC-058-1 WCMC-RCC-058-2 WCMC-RCC-057-1 WCMC-RCC-051-1 WCMC-RCC-050-1 WCMC-RCC-050-2 WCMC-RCC-048-1 WCMC-RCC-048-2 WCMC-RCC-047-1 WCMC-RCC-045-1 WCMC-RCC-044-1 WCMC-RCC-043-1 WCMC-RCC-041-1 WCMC-RCC-039-1 WCMC-RCC-036-2 WCMC-RCC-035-1 WCMC-RCC-034-1 WCMC-RCC-033-1 WCMC-RCC-033-2 WCMC-RCC-032-1 WCMC-RCC-030-1 WCMC-RCC-030-2 WCMC-RCC-029-1 WCMC-RCC-029-2 WCMC-RCC-026-1 WCMC-RCC-024-1 WCMC-RCC-023-1 WCMC-RCC-022-1 WCMC-RCC-008-1 WCMC-RCC-008-2 WCMC-RCC-008-3 WCMC-RCC-008-4 WCMC-RCC-019-1 WCMC-RCC-015-1 WCMC-RCC-015-2 WCMC-RCC-015-3 WCMC-RCC-015-4 WCMC-RCC-014-1 WCMC-RCC-013-1 WCMC-RCC-007-1 WCMC-RCC-007-2 WCMC-RCC-007-3 WCMC-RCC-007-4 WCMC-RCC-007-5 WCMC-RCC-007-6 WCMC-RCC-007-7 WCMC-RCC-086-1 WCMC-RCC-010-1 WCMC-RCC-006-1 WCMC-RCC-006-2 WCMC-RCC-006-3 WCMC-RCC-003-1 WCMC-RCC-002-1 WCMC-RCC-001-1 \ No newline at end of file +case_list_ids: WCMC-RCC-048-2 WCMC-RCC-084-1 WCMC-RCC-050-1 WCMC-RCC-050-2 WCMC-RCC-084-2 WCMC-RCC-051-1 WCMC-RCC-033-1 WCMC-RCC-048-1 WCMC-RCC-035-1 WCMC-RCC-058-1 WCMC-RCC-057-1 WCMC-RCC-078-1 WCMC-RCC-085-1 WCMC-RCC-045-1 WCMC-RCC-008-1 WCMC-RCC-047-1 WCMC-RCC-036-1 WCMC-RCC-060-1 WCMC-RCC-065-1 WCMC-RCC-065-2 WCMC-RCC-034-1 WCMC-RCC-030-2 WCMC-RCC-036-2 WCMC-RCC-044-1 WCMC-RCC-030-1 WCMC-RCC-032-1 WCMC-RCC-001-1 WCMC-RCC-019-1 WCMC-RCC-014-1 WCMC-RCC-058-2 WCMC-RCC-033-2 WCMC-RCC-015-1 WCMC-RCC-029-1 WCMC-RCC-029-2 WCMC-RCC-015-2 WCMC-RCC-007-4 WCMC-RCC-007-5 WCMC-RCC-006-3 WCMC-RCC-007-7 WCMC-RCC-007-1 WCMC-RCC-069-1 WCMC-RCC-008-4 WCMC-RCC-007-6 WCMC-RCC-006-1 WCMC-RCC-024-1 WCMC-RCC-006-2 WCMC-RCC-008-3 WCMC-RCC-008-2 WCMC-RCC-015-4 WCMC-RCC-022-1 WCMC-RCC-007-2 WCMC-RCC-026-1 WCMC-RCC-086-1 WCMC-RCC-039-1 WCMC-RCC-077-1 WCMC-RCC-007-3 WCMC-RCC-023-1 WCMC-RCC-015-3 WCMC-RCC-043-1 WCMC-RCC-002-1 WCMC-RCC-010-1 WCMC-RCC-081-1 WCMC-RCC-003-1 WCMC-RCC-013-1 WCMC-RCC-041-1 WCMC-RCC-074-2 WCMC-RCC-074-1 diff --git a/public/ccrcc_wcm_2022/data_mutations.txt b/public/ccrcc_wcm_2022/data_mutations.txt index e3d256ad4c..09b68a3df1 100644 --- a/public/ccrcc_wcm_2022/data_mutations.txt +++ b/public/ccrcc_wcm_2022/data_mutations.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:7685cc040ab84fa1718cfe06ef6aa9910aef38da6d1d1829d393ebaf7b54ddba -size 9302041 +oid sha256:34f91db7f03dfcc4492e387a54c1fd9df740f8c03afe46dfcd660b94a71a5eac +size 19490246 From 2cdbf7e29b613eaf88ed34e0657262b2f383c80f Mon Sep 17 00:00:00 2001 From: RAlhamad Date: Mon, 21 Aug 2023 09:51:37 -0400 Subject: [PATCH 5/5] Error fix --- public/ccrcc_wcm_2022/case_lists/cases_all.txt | 6 ------ 1 file changed, 6 deletions(-) delete mode 100644 public/ccrcc_wcm_2022/case_lists/cases_all.txt diff --git a/public/ccrcc_wcm_2022/case_lists/cases_all.txt b/public/ccrcc_wcm_2022/case_lists/cases_all.txt deleted file mode 100644 index 15718fdfc6..0000000000 --- a/public/ccrcc_wcm_2022/case_lists/cases_all.txt +++ /dev/null @@ -1,6 +0,0 @@ -cancer_study_identifier: ccrcc_wcm_2022 -stable_id: ccrcc_wcm_2022_all -case_list_name: All samples -case_list_description: All samples (67 samples) -case_list_category: all_cases_in_study -case_list_ids: WCMC-RCC-036-1 WCMC-RCC-036-2 WCMC-RCC-084-2 WCMC-RCC-048-1 WCMC-RCC-035-1 WCMC-RCC-014-1 WCMC-RCC-057-1 WCMC-RCC-078-1 WCMC-RCC-045-1 WCMC-RCC-060-1 WCMC-RCC-043-1 WCMC-RCC-034-1 WCMC-RCC-032-1 WCMC-RCC-001-1 WCMC-RCC-033-1 WCMC-RCC-058-1 WCMC-RCC-058-2 WCMC-RCC-033-2 WCMC-RCC-015-1 WCMC-RCC-007-1 WCMC-RCC-007-2 WCMC-RCC-015-2 WCMC-RCC-007-4 WCMC-RCC-007-5 WCMC-RCC-006-3 WCMC-RCC-007-7 WCMC-RCC-006-1 WCMC-RCC-069-1 WCMC-RCC-007-6 WCMC-RCC-008-4 WCMC-RCC-008-3 WCMC-RCC-008-2 WCMC-RCC-008-1 WCMC-RCC-022-1 WCMC-RCC-081-1 WCMC-RCC-086-1 WCMC-RCC-023-1 WCMC-RCC-015-3 WCMC-RCC-010-1 WCMC-RCC-013-1 WCMC-RCC-041-1 WCMC-RCC-048-2 WCMC-RCC-084-1 WCMC-RCC-050-1 WCMC-RCC-050-2 WCMC-RCC-051-1 WCMC-RCC-085-1 WCMC-RCC-047-1 WCMC-RCC-065-1 WCMC-RCC-065-2 WCMC-RCC-030-2 WCMC-RCC-044-1 WCMC-RCC-030-1 WCMC-RCC-019-1 WCMC-RCC-029-1 WCMC-RCC-029-2 WCMC-RCC-015-4 WCMC-RCC-024-1 WCMC-RCC-026-1 WCMC-RCC-006-2 WCMC-RCC-077-1 WCMC-RCC-003-1 WCMC-RCC-002-1 WCMC-RCC-007-3 WCMC-RCC-039-1 WCMC-RCC-074-2 WCMC-RCC-074-1