From 43913745de8a9796449925d136ce0943a1f7402d Mon Sep 17 00:00:00 2001 From: Justin Jao Date: Thu, 31 Aug 2023 01:02:42 -0700 Subject: [PATCH] test --- public/acbc_mskcc_2015/LICENSE | 1 + public/acbc_mskcc_2015/case_lists/cases_all.txt | 6 ++++++ public/acbc_mskcc_2015/case_lists/cases_cna.txt | 6 ++++++ public/acbc_mskcc_2015/case_lists/cases_cnaseq.txt | 6 ++++++ public/acbc_mskcc_2015/case_lists/cases_sequenced.txt | 6 ++++++ public/acbc_mskcc_2015/case_lists/cases_sv.txt | 6 ++++++ public/acbc_mskcc_2015/data_clinical_patient.txt | 3 +++ public/acbc_mskcc_2015/data_clinical_sample.txt | 3 +++ public/acbc_mskcc_2015/data_cna.txt | 3 +++ public/acbc_mskcc_2015/data_gene_panel_matrix.txt | 3 +++ public/acbc_mskcc_2015/data_mutations.txt | 3 +++ public/acbc_mskcc_2015/data_sv.txt | 3 +++ public/acbc_mskcc_2015/meta_clinical_patient.txt | 4 ++++ public/acbc_mskcc_2015/meta_clinical_sample.txt | 4 ++++ public/acbc_mskcc_2015/meta_cna.txt | 8 ++++++++ public/acbc_mskcc_2015/meta_gene_panel_matrix.txt | 4 ++++ public/acbc_mskcc_2015/meta_mutations.txt | 8 ++++++++ public/acbc_mskcc_2015/meta_study.txt | 9 +++++++++ public/acbc_mskcc_2015/meta_sv.txt | 8 ++++++++ 19 files changed, 94 insertions(+) create mode 100644 public/acbc_mskcc_2015/LICENSE create mode 100755 public/acbc_mskcc_2015/case_lists/cases_all.txt create mode 100755 public/acbc_mskcc_2015/case_lists/cases_cna.txt create mode 100755 public/acbc_mskcc_2015/case_lists/cases_cnaseq.txt create mode 100755 public/acbc_mskcc_2015/case_lists/cases_sequenced.txt create mode 100755 public/acbc_mskcc_2015/case_lists/cases_sv.txt create mode 100644 public/acbc_mskcc_2015/data_clinical_patient.txt create mode 100644 public/acbc_mskcc_2015/data_clinical_sample.txt create mode 100644 public/acbc_mskcc_2015/data_cna.txt create mode 100755 public/acbc_mskcc_2015/data_gene_panel_matrix.txt create mode 100644 public/acbc_mskcc_2015/data_mutations.txt create mode 100755 public/acbc_mskcc_2015/data_sv.txt create mode 100644 public/acbc_mskcc_2015/meta_clinical_patient.txt create mode 100644 public/acbc_mskcc_2015/meta_clinical_sample.txt create mode 100644 public/acbc_mskcc_2015/meta_cna.txt create mode 100755 public/acbc_mskcc_2015/meta_gene_panel_matrix.txt create mode 100644 public/acbc_mskcc_2015/meta_mutations.txt create mode 100644 public/acbc_mskcc_2015/meta_study.txt create mode 100755 public/acbc_mskcc_2015/meta_sv.txt diff --git a/public/acbc_mskcc_2015/LICENSE b/public/acbc_mskcc_2015/LICENSE new file mode 100644 index 0000000000..d5f3c4b535 --- /dev/null +++ b/public/acbc_mskcc_2015/LICENSE @@ -0,0 +1 @@ +The data are available under the ODC Open Database License (ODbL)(http://opendatacommons.org/licenses/odbl/1.0/) (summary available here: http://www.opendatacommons.org/licenses/odbl/1-0/summary/): you are free to share and modify the data so long as you attribute any public use of the database, or works produced from the database; keep the resulting data-sets open; and offer your shared or adapted version of the data-set under the same ODbL license. diff --git a/public/acbc_mskcc_2015/case_lists/cases_all.txt b/public/acbc_mskcc_2015/case_lists/cases_all.txt new file mode 100755 index 0000000000..a10bf02786 --- /dev/null +++ b/public/acbc_mskcc_2015/case_lists/cases_all.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: acbc_mskcc_2015 +stable_id: acbc_mskcc_2015_all +case_list_name: All samples +case_list_description: All samples (12 samples) +case_list_category: all_cases_in_study +case_list_ids: AdCC2T AdCC3T AdCC8T AdCC1T AdCC11T AdCC10T AdCC6T AdCC5T AdCC32T AdCC4T AdCC9T AdCC12T diff --git a/public/acbc_mskcc_2015/case_lists/cases_cna.txt b/public/acbc_mskcc_2015/case_lists/cases_cna.txt new file mode 100755 index 0000000000..a0a0ec3b34 --- /dev/null +++ b/public/acbc_mskcc_2015/case_lists/cases_cna.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: acbc_mskcc_2015 +stable_id: acbc_mskcc_2015_cna +case_list_name: Samples with CNA data +case_list_description: Samples with CNA data (12 samples) +case_list_category: all_cases_with_cna_data +case_list_ids: AdCC2T AdCC3T AdCC8T AdCC1T AdCC11T AdCC10T AdCC6T AdCC5T AdCC32T AdCC4T AdCC9T AdCC12T diff --git a/public/acbc_mskcc_2015/case_lists/cases_cnaseq.txt b/public/acbc_mskcc_2015/case_lists/cases_cnaseq.txt new file mode 100755 index 0000000000..16aba12553 --- /dev/null +++ b/public/acbc_mskcc_2015/case_lists/cases_cnaseq.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: acbc_mskcc_2015 +stable_id: acbc_mskcc_2015_cnaseq +case_list_name: Samples with mutation and CNA data +case_list_description: Samples with mutation and CNA data (12 samples) +case_list_category: all_cases_with_mutation_and_cna_data +case_list_ids: AdCC10T AdCC3T AdCC8T AdCC1T AdCC11T AdCC2T AdCC6T AdCC5T AdCC32T AdCC4T AdCC9T AdCC12T diff --git a/public/acbc_mskcc_2015/case_lists/cases_sequenced.txt b/public/acbc_mskcc_2015/case_lists/cases_sequenced.txt new file mode 100755 index 0000000000..36bad90999 --- /dev/null +++ b/public/acbc_mskcc_2015/case_lists/cases_sequenced.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: acbc_mskcc_2015 +stable_id: acbc_mskcc_2015_sequenced +case_list_name: Samples with mutation data +case_list_description: Samples with mutation data (12 samples) +case_list_category: all_cases_with_mutation_data +case_list_ids: AdCC10T AdCC3T AdCC8T AdCC1T AdCC11T AdCC2T AdCC6T AdCC5T AdCC32T AdCC4T AdCC9T AdCC12T diff --git a/public/acbc_mskcc_2015/case_lists/cases_sv.txt b/public/acbc_mskcc_2015/case_lists/cases_sv.txt new file mode 100755 index 0000000000..1bc03c6ff4 --- /dev/null +++ b/public/acbc_mskcc_2015/case_lists/cases_sv.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: acbc_mskcc_2015 +stable_id: acbc_mskcc_2015_sv +case_list_name: Samples with SV data +case_list_description: All samples (12 samples) +case_list_category: all_cases_with_sv_data +case_list_ids: AdCC10T AdCC3T AdCC8T AdCC1T AdCC11T AdCC2T AdCC6T AdCC5T AdCC32T AdCC4T AdCC9T AdCC12T \ No newline at end of file diff --git a/public/acbc_mskcc_2015/data_clinical_patient.txt b/public/acbc_mskcc_2015/data_clinical_patient.txt new file mode 100644 index 0000000000..79a1521f73 --- /dev/null +++ b/public/acbc_mskcc_2015/data_clinical_patient.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:1270a34e9e9b2ec1f6999da9f9874b32398ad4fd64eb2a7c0151a6cd69a9fcbc +size 2934 diff --git a/public/acbc_mskcc_2015/data_clinical_sample.txt b/public/acbc_mskcc_2015/data_clinical_sample.txt new file mode 100644 index 0000000000..838db63e89 --- /dev/null +++ b/public/acbc_mskcc_2015/data_clinical_sample.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:fffcc13f7e2a59144dadb9bd2aa2ca3f30879c53601e0f541c2a916dfaaa026f +size 4431 diff --git a/public/acbc_mskcc_2015/data_cna.txt b/public/acbc_mskcc_2015/data_cna.txt new file mode 100644 index 0000000000..b028d34d22 --- /dev/null +++ b/public/acbc_mskcc_2015/data_cna.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:97d1c4c1760c1ec21f4de06446ccc396de11f22903e171ebdf20d91d1798c0e1 +size 70579 diff --git a/public/acbc_mskcc_2015/data_gene_panel_matrix.txt b/public/acbc_mskcc_2015/data_gene_panel_matrix.txt new file mode 100755 index 0000000000..3523fdd8a8 --- /dev/null +++ b/public/acbc_mskcc_2015/data_gene_panel_matrix.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:34a137eca2acfde89927c8ffadef30ef4cbcfb6cc35ee636663ce4c8684168b4 +size 275 diff --git a/public/acbc_mskcc_2015/data_mutations.txt b/public/acbc_mskcc_2015/data_mutations.txt new file mode 100644 index 0000000000..19249e2037 --- /dev/null +++ b/public/acbc_mskcc_2015/data_mutations.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:dea6ea3c1ee31cacda739c3ae65a47b053511f5bcc21b0a467eca5a9591fcf34 +size 71401 diff --git a/public/acbc_mskcc_2015/data_sv.txt b/public/acbc_mskcc_2015/data_sv.txt new file mode 100755 index 0000000000..82c09ccb13 --- /dev/null +++ b/public/acbc_mskcc_2015/data_sv.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:440f85a63a66bb13932bcae363352b0b29d7548df002c2281101ac2110cbf60c +size 968 diff --git a/public/acbc_mskcc_2015/meta_clinical_patient.txt b/public/acbc_mskcc_2015/meta_clinical_patient.txt new file mode 100644 index 0000000000..b4904ece4f --- /dev/null +++ b/public/acbc_mskcc_2015/meta_clinical_patient.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: acbc_mskcc_2015 +genetic_alteration_type: CLINICAL +datatype: PATIENT_ATTRIBUTES +data_filename: data_clinical_patient.txt \ No newline at end of file diff --git a/public/acbc_mskcc_2015/meta_clinical_sample.txt b/public/acbc_mskcc_2015/meta_clinical_sample.txt new file mode 100644 index 0000000000..504ff89248 --- /dev/null +++ b/public/acbc_mskcc_2015/meta_clinical_sample.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: acbc_mskcc_2015 +genetic_alteration_type: CLINICAL +datatype: SAMPLE_ATTRIBUTES +data_filename: data_clinical_sample.txt \ No newline at end of file diff --git a/public/acbc_mskcc_2015/meta_cna.txt b/public/acbc_mskcc_2015/meta_cna.txt new file mode 100644 index 0000000000..80eec94c51 --- /dev/null +++ b/public/acbc_mskcc_2015/meta_cna.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: acbc_mskcc_2015 +genetic_alteration_type: COPY_NUMBER_ALTERATION +datatype: DISCRETE +stable_id: cna +show_profile_in_analysis_tab: true +profile_description: Putative copy-number from GISTIC 2.0. Values: -2 = homozygous deletion; -1 = hemizygous deletion; 0 = neutral / no change; 1 = gain; 2 = high level amplification. +profile_name: Putative copy-number alterations from GISTIC +data_filename: data_cna.txt diff --git a/public/acbc_mskcc_2015/meta_gene_panel_matrix.txt b/public/acbc_mskcc_2015/meta_gene_panel_matrix.txt new file mode 100755 index 0000000000..4eaa1d2dce --- /dev/null +++ b/public/acbc_mskcc_2015/meta_gene_panel_matrix.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: acbc_mskcc_2015 +genetic_alteration_type: GENE_PANEL_MATRIX +datatype: GENE_PANEL_MATRIX +data_filename: data_gene_panel_matrix.txt diff --git a/public/acbc_mskcc_2015/meta_mutations.txt b/public/acbc_mskcc_2015/meta_mutations.txt new file mode 100644 index 0000000000..5ca3c11a46 --- /dev/null +++ b/public/acbc_mskcc_2015/meta_mutations.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: acbc_mskcc_2015 +genetic_alteration_type: MUTATION_EXTENDED +datatype: MAF +stable_id: mutations +show_profile_in_analysis_tab: true +profile_description: Whole exome sequencing of 12 breast AdCCs. +profile_name: Mutations +data_filename: data_mutations.txt diff --git a/public/acbc_mskcc_2015/meta_study.txt b/public/acbc_mskcc_2015/meta_study.txt new file mode 100644 index 0000000000..2438b12a93 --- /dev/null +++ b/public/acbc_mskcc_2015/meta_study.txt @@ -0,0 +1,9 @@ +type_of_cancer: acbc +cancer_study_identifier: acbc_mskcc_2015 +name: Adenoid Cystic Carcinoma of the Breast (MSK, J Pathol. 2015) +description: Whole exome sequencing of 12 breast AdCCs. +short_name: ACBC (MSKCC/Breast 2015) +public_study: true +pmid: 26095796 +citation: Martelotto et al. J Pathol 2015 +groups: PUBLIC;ACYC \ No newline at end of file diff --git a/public/acbc_mskcc_2015/meta_sv.txt b/public/acbc_mskcc_2015/meta_sv.txt new file mode 100755 index 0000000000..dc0c8ba4ea --- /dev/null +++ b/public/acbc_mskcc_2015/meta_sv.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: acbc_mskcc_2015 +genetic_alteration_type: STRUCTURAL_VARIANT +datatype: SV +stable_id: structural_variants +show_profile_in_analysis_tab: true +profile_name: Structural variants +profile_description: Structural Variant Data. +data_filename: data_sv.txt \ No newline at end of file