diff --git a/public/gbm_tcga_pan_can_atlas_2018/README.md b/public/gbm_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/gbm_tcga_pan_can_atlas_2018/README.md +++ b/public/gbm_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/gbm_tcga_pan_can_atlas_2018/data_clinical_patient.txt b/public/gbm_tcga_pan_can_atlas_2018/data_clinical_patient.txt index 66ef8a7dbb..93d9ef45a6 100644 --- a/public/gbm_tcga_pan_can_atlas_2018/data_clinical_patient.txt +++ b/public/gbm_tcga_pan_can_atlas_2018/data_clinical_patient.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:0d10a64d6946b1e625c82a898c92a7353ba866ef1cecf1d9a777cb1076b72cb0 -size 115588 +oid sha256:5d0234de398cd1fd55e17bc34eb47781fddd47cbb3f2168e54f535dafa31d144 +size 118038 diff --git a/public/gbm_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt b/public/gbm_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt new file mode 100644 index 0000000000..4e29065d7b --- /dev/null +++ b/public/gbm_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:29673734391592c0b542a742decef5059438db4cde48d60ae0026c3292635024 +size 28537 diff --git a/public/gbm_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt b/public/gbm_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt new file mode 100644 index 0000000000..4e3678bd4a --- /dev/null +++ b/public/gbm_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt @@ -0,0 +1,11 @@ +cancer_study_identifier: gbm_tcga_pan_can_atlas_2018 +genetic_alteration_type: GENERIC_ASSAY +generic_assay_type: GENETIC_ANCESTRY +datatype: LIMIT-VALUE +stable_id: genetic_ancestry +profile_name: Genetic Ancestry +profile_description: Genetic ancestries were determined using five different methods as described in Carrot-Zhang et al (2020). These consensus calls were created based on the ancestral population that received the majority of assignments for each patient. The original data is here. +data_filename: data_genetic_ancestry.txt +show_profile_in_analysis_tab: true +generic_entity_meta_properties: NAME +value_sort_order: ASC diff --git a/public/hnsc_tcga_pan_can_atlas_2018/README.md b/public/hnsc_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/hnsc_tcga_pan_can_atlas_2018/README.md +++ b/public/hnsc_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/hnsc_tcga_pan_can_atlas_2018/data_clinical_patient.txt b/public/hnsc_tcga_pan_can_atlas_2018/data_clinical_patient.txt index 70d65b30a7..b92108ddcc 100644 --- a/public/hnsc_tcga_pan_can_atlas_2018/data_clinical_patient.txt +++ b/public/hnsc_tcga_pan_can_atlas_2018/data_clinical_patient.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:5a5d8b4776704bf66b2f8e8a1804db47da98ba455dd0ae721974bc66fbd12c41 -size 156380 +oid sha256:10e6eefdf38c9fd3bd5eb160535619c54a519fb86d0eca99d708f342dd23024f +size 158624 diff --git a/public/hnsc_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt b/public/hnsc_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt new file mode 100644 index 0000000000..49434638e3 --- /dev/null +++ b/public/hnsc_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f3b1a1bcc613bf5cad64c202dd876a1856ecee89940f0b1b00cddd65698d5d47 +size 29910 diff --git a/public/hnsc_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt b/public/hnsc_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt new file mode 100644 index 0000000000..4baf167e51 --- /dev/null +++ b/public/hnsc_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt @@ -0,0 +1,11 @@ +cancer_study_identifier: hnsc_tcga_pan_can_atlas_2018 +genetic_alteration_type: GENERIC_ASSAY +generic_assay_type: GENETIC_ANCESTRY +datatype: LIMIT-VALUE +stable_id: genetic_ancestry +profile_name: Genetic Ancestry +profile_description: Genetic ancestries were determined using five different methods as described in Carrot-Zhang et al (2020). These consensus calls were created based on the ancestral population that received the majority of assignments for each patient. The original data is here. +data_filename: data_genetic_ancestry.txt +show_profile_in_analysis_tab: true +generic_entity_meta_properties: NAME +value_sort_order: ASC diff --git a/public/kich_tcga_pan_can_atlas_2018/README.md b/public/kich_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/kich_tcga_pan_can_atlas_2018/README.md +++ b/public/kich_tcga_pan_can_atlas_2018/README.md @@ -7,4 +7,22 @@ - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type. **Data Transformation** -- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) \ No newline at end of file +- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + +### The Genetic Ancestry data: + + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 +- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type. + + +### The Methylation data: + +**Data Source** +- GDAC Firehose: https://gdc.cancer.gov/node/977 +- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type. + +**Data Transformation** + - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file diff --git a/public/kich_tcga_pan_can_atlas_2018/data_clinical_patient.txt b/public/kich_tcga_pan_can_atlas_2018/data_clinical_patient.txt index 36741f8008..dc55ec0f48 100644 --- a/public/kich_tcga_pan_can_atlas_2018/data_clinical_patient.txt +++ b/public/kich_tcga_pan_can_atlas_2018/data_clinical_patient.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:6324ffc8153494cfee4e603157a4384a2ae03b9678fc51f9d92cf830745014c3 -size 24526 +oid sha256:4ef7ae1e29eb9b1e24f3ace412cf343b6267e2750cf643c443ff2f1e1fd11bda +size 24868 diff --git a/public/kich_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt b/public/kich_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt new file mode 100644 index 0000000000..e110587d76 --- /dev/null +++ b/public/kich_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:caf980b6340682d6886444e485d5bbcb01abe3356ee43e3a619f044bf895f8b6 +size 4063 diff --git a/public/kich_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt b/public/kich_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt new file mode 100644 index 0000000000..238aa436f8 --- /dev/null +++ b/public/kich_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt @@ -0,0 +1,11 @@ +cancer_study_identifier: kich_tcga_pan_can_atlas_2018 +genetic_alteration_type: GENERIC_ASSAY +generic_assay_type: GENETIC_ANCESTRY +datatype: LIMIT-VALUE +stable_id: genetic_ancestry +profile_name: Genetic Ancestry +profile_description: Genetic ancestries were determined using five different methods as described in Carrot-Zhang et al (2020). These consensus calls were created based on the ancestral population that received the majority of assignments for each patient. The original data is here. +data_filename: data_genetic_ancestry.txt +show_profile_in_analysis_tab: true +generic_entity_meta_properties: NAME +value_sort_order: ASC \ No newline at end of file