diff --git a/public/coadread_tcga_pan_can_atlas_2018/README.md b/public/coadread_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/coadread_tcga_pan_can_atlas_2018/README.md +++ b/public/coadread_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/coadread_tcga_pan_can_atlas_2018/data_clinical_patient.txt b/public/coadread_tcga_pan_can_atlas_2018/data_clinical_patient.txt index 9cf1ebe2d0..dddb1d4d8e 100644 --- a/public/coadread_tcga_pan_can_atlas_2018/data_clinical_patient.txt +++ b/public/coadread_tcga_pan_can_atlas_2018/data_clinical_patient.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:0d03471199372e0f43dea0e271c26a8aa9d00bc70a276ccb8c9f580a7adc988e -size 172415 +oid sha256:c19f9f91f47db6a48d250c8a6c59a8c5068a1e20c9798083a41de81d48630d3d +size 175005 diff --git a/public/coadread_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt b/public/coadread_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt new file mode 100644 index 0000000000..1de5a28860 --- /dev/null +++ b/public/coadread_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:84e74a885e149dd4150ffc56a6186cf6eb91f5711bc3defed346e34908d4f78b +size 33217 diff --git a/public/coadread_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt b/public/coadread_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt new file mode 100644 index 0000000000..f76f51d56e --- /dev/null +++ b/public/coadread_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt @@ -0,0 +1,11 @@ +cancer_study_identifier: coadread_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 diff --git a/public/dlbc_tcga_pan_can_atlas_2018/README.md b/public/dlbc_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/dlbc_tcga_pan_can_atlas_2018/README.md +++ b/public/dlbc_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/dlbc_tcga_pan_can_atlas_2018/data_clinical_patient.txt b/public/dlbc_tcga_pan_can_atlas_2018/data_clinical_patient.txt index 12dd287f62..f100c0e1a5 100644 --- a/public/dlbc_tcga_pan_can_atlas_2018/data_clinical_patient.txt +++ b/public/dlbc_tcga_pan_can_atlas_2018/data_clinical_patient.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:4b6bc8dc60c779c146cba5422b19f6a33eb8ab94f554bc832c198a3b46af205f -size 19456 +oid sha256:23696807805d4515f9f0073121659d4bbb59c23ee8cee48278cc96a09d857c87 +size 19750 diff --git a/public/dlbc_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt b/public/dlbc_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt new file mode 100644 index 0000000000..3c2586b8be --- /dev/null +++ b/public/dlbc_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ccf40e88a5720892c7c3a9baedc04128c8370dad90a533b08114390780a785b2 +size 2973 diff --git a/public/dlbc_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt b/public/dlbc_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt new file mode 100644 index 0000000000..a8b9e782fe --- /dev/null +++ b/public/dlbc_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt @@ -0,0 +1,11 @@ +cancer_study_identifier: dlbc_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/esca_tcga_pan_can_atlas_2018/README.md b/public/esca_tcga_pan_can_atlas_2018/README.md index b64cd59ae4..4372ea260f 100644 --- a/public/esca_tcga_pan_can_atlas_2018/README.md +++ b/public/esca_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/esca_tcga_pan_can_atlas_2018/data_clinical_patient.txt b/public/esca_tcga_pan_can_atlas_2018/data_clinical_patient.txt index c9286eab57..0fa714b967 100644 --- a/public/esca_tcga_pan_can_atlas_2018/data_clinical_patient.txt +++ b/public/esca_tcga_pan_can_atlas_2018/data_clinical_patient.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:a741aab153e054c52c7ca4966adb500b69af1b8cc71d39533e833e273a74086f -size 57824 +oid sha256:a6a25df2143c0ae49312fb5c46455143ae8156e9e1b03850926bbef07fb73ed1 +size 58662 diff --git a/public/esca_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt b/public/esca_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt new file mode 100644 index 0000000000..02924db79f --- /dev/null +++ b/public/esca_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:314faf4e3df1fa7b3429fd4d6c0dd7dd1cb05915ead847d3abe0ab16c1138d00 +size 10733 diff --git a/public/esca_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt b/public/esca_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt new file mode 100644 index 0000000000..556f40f879 --- /dev/null +++ b/public/esca_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt @@ -0,0 +1,11 @@ +cancer_study_identifier: esca_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