Merge pull request #2094 from cBioPortal/add_study

msk_chord_2024: move files to Datahub
cBioPortal · Nov 6, 2024 · 60938c2 · 60938c2
2 parents 847f45c + 3cb867d
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diff --git a/public/msk_chord_2024/LICENSE b/public/msk_chord_2024/LICENSE
diff --git a/public/msk_chord_2024/Readme.txt b/public/msk_chord_2024/Readme.txt
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+Gene panels for this study can be found here: https://github.com/cBioPortal/datahub/tree/master/reference_data/gene_panels
diff --git a/public/msk_chord_2024/case_lists/cases_all.txt b/public/msk_chord_2024/case_lists/cases_all.txt
diff --git a/public/msk_chord_2024/case_lists/cases_cna.txt b/public/msk_chord_2024/case_lists/cases_cna.txt
diff --git a/public/msk_chord_2024/case_lists/cases_cnaseq.txt b/public/msk_chord_2024/case_lists/cases_cnaseq.txt
diff --git a/public/msk_chord_2024/case_lists/cases_sequenced.txt b/public/msk_chord_2024/case_lists/cases_sequenced.txt
diff --git a/public/msk_chord_2024/case_lists/cases_sv.txt b/public/msk_chord_2024/case_lists/cases_sv.txt
diff --git a/public/msk_chord_2024/data_clinical_patient.txt b/public/msk_chord_2024/data_clinical_patient.txt
diff --git a/public/msk_chord_2024/data_clinical_sample.txt b/public/msk_chord_2024/data_clinical_sample.txt
diff --git a/public/msk_chord_2024/data_cna.txt b/public/msk_chord_2024/data_cna.txt
diff --git a/public/msk_chord_2024/data_cna_hg19.seg b/public/msk_chord_2024/data_cna_hg19.seg
diff --git a/public/msk_chord_2024/data_gene_panel_matrix.txt b/public/msk_chord_2024/data_gene_panel_matrix.txt
diff --git a/public/msk_chord_2024/data_mutations.txt b/public/msk_chord_2024/data_mutations.txt
diff --git a/public/msk_chord_2024/data_sv.txt b/public/msk_chord_2024/data_sv.txt
diff --git a/public/msk_chord_2024/data_timeline_cancer_presence.txt b/public/msk_chord_2024/data_timeline_cancer_presence.txt
diff --git a/public/msk_chord_2024/data_timeline_diagnosis.txt b/public/msk_chord_2024/data_timeline_diagnosis.txt
diff --git a/public/msk_chord_2024/data_timeline_gleason.txt b/public/msk_chord_2024/data_timeline_gleason.txt
diff --git a/public/msk_chord_2024/data_timeline_mmr.txt b/public/msk_chord_2024/data_timeline_mmr.txt
diff --git a/public/msk_chord_2024/data_timeline_pdl1.txt b/public/msk_chord_2024/data_timeline_pdl1.txt
diff --git a/public/msk_chord_2024/data_timeline_performance_status.txt b/public/msk_chord_2024/data_timeline_performance_status.txt
diff --git a/public/msk_chord_2024/data_timeline_prior_meds.txt b/public/msk_chord_2024/data_timeline_prior_meds.txt
diff --git a/public/msk_chord_2024/data_timeline_progression.txt b/public/msk_chord_2024/data_timeline_progression.txt
diff --git a/public/msk_chord_2024/data_timeline_radiation.txt b/public/msk_chord_2024/data_timeline_radiation.txt
diff --git a/public/msk_chord_2024/data_timeline_specimen.txt b/public/msk_chord_2024/data_timeline_specimen.txt
diff --git a/public/msk_chord_2024/data_timeline_specimen_surgery.txt b/public/msk_chord_2024/data_timeline_specimen_surgery.txt
diff --git a/public/msk_chord_2024/data_timeline_surgery.txt b/public/msk_chord_2024/data_timeline_surgery.txt
diff --git a/public/msk_chord_2024/data_timeline_treatment.txt b/public/msk_chord_2024/data_timeline_treatment.txt
diff --git a/public/msk_chord_2024/data_timeline_tumor_markers.txt b/public/msk_chord_2024/data_timeline_tumor_markers.txt
diff --git a/public/msk_chord_2024/data_timeline_tumor_sites.txt b/public/msk_chord_2024/data_timeline_tumor_sites.txt
diff --git a/public/msk_chord_2024/meta_clinical_patient.txt b/public/msk_chord_2024/meta_clinical_patient.txt
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+cancer_study_identifier: msk_chord_2024
+genetic_alteration_type: CLINICAL
+datatype: PATIENT_ATTRIBUTES
+data_filename: data_clinical_patient.txt
diff --git a/public/msk_chord_2024/meta_clinical_sample.txt b/public/msk_chord_2024/meta_clinical_sample.txt
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+cancer_study_identifier: msk_chord_2024
+genetic_alteration_type: CLINICAL
+datatype: SAMPLE_ATTRIBUTES
+data_filename: data_clinical_sample.txt
diff --git a/public/msk_chord_2024/meta_cna.txt b/public/msk_chord_2024/meta_cna.txt
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+cancer_study_identifier: msk_chord_2024
+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/msk_chord_2024/meta_cna_hg19_seg.txt b/public/msk_chord_2024/meta_cna_hg19_seg.txt
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+cancer_study_identifier: msk_chord_2024
+genetic_alteration_type: COPY_NUMBER_ALTERATION
+datatype: SEG
+show_profile_in_analysis_tab: false
+description: Somatic CNA data (copy number ratio from tumor samples minus ratio from matched normals).
+profile_name: Segment data values
+reference_genome_id: hg19
+data_filename: data_cna_hg19.seg
diff --git a/public/msk_chord_2024/meta_gene_panel_matrix.txt b/public/msk_chord_2024/meta_gene_panel_matrix.txt
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+cancer_study_identifier: msk_chord_2024
+genetic_alteration_type: GENE_PANEL_MATRIX
+datatype: GENE_PANEL_MATRIX
+data_filename: data_gene_panel_matrix.txt
diff --git a/public/msk_chord_2024/meta_mutations.txt b/public/msk_chord_2024/meta_mutations.txt
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+cancer_study_identifier: msk_chord_2024
+genetic_alteration_type: MUTATION_EXTENDED
+datatype: MAF
+stable_id: mutations
+show_profile_in_analysis_tab: true
+profile_description: Mutation data.
+profile_name: Mutations
+data_filename: data_mutations.txt
diff --git a/public/msk_chord_2024/meta_study.txt b/public/msk_chord_2024/meta_study.txt
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+type_of_cancer: mixed
+cancer_study_identifier: msk_chord_2024
+name: MSK CHORD (MSK, 2024)
+description: Targeted sequencing of 25040 tumors from 24950 patients and their matched normals via MSK-IMPACT, along with clinical annotations, some of which are derived from natural language processing (denoted NLP). This data is available under the <a href="https://creativecommons.org/licenses/by-nc-nd/4.0/deed.en">Creative Commons BY-NC-ND 4.0 license</a>. For commercial use, please contact [email protected]
diff --git a/public/msk_chord_2024/meta_sv.txt b/public/msk_chord_2024/meta_sv.txt
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+cancer_study_identifier: msk_chord_2024
+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
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		Gene panels for this study can be found here: https://github.com/cBioPortal/datahub/tree/master/reference_data/gene_panels