machine-readable information for the TCGA and CPTAC datasets, mirrored from other sources. The aim of this repo is to
- provide standardized and slightly cleaned data
- ease the load on the original servers
| file name | changes made | retrieved from |
|---|---|---|
| tcga/tcga-tumor-types.csv | none | https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tcga-study-abbreviations |
| tcga/immune.xlsx | none | https://www.cell.com/cms/10.1016/j.immuni.2018.03.023/attachment/1b63d4bc-af31-4a23-99bb-7ca23c7b4e0a/mmc2.xlsx |
| tcga/outcome.xlsx | reordered sheets, removed index | https://api.gdc.cancer.gov/data/1b5f413e-a8d1-4d10-92eb-7c4ae739ed81 |
| tcga/tissue-sites.csv | none | https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tissue-source-site-codes |
| tcga/cbio_clinical.xlsx | none | https://www.cbioportal.org/study/summary?id=laml_tcga_pan_can_atlas_2018 |
| tcga/tcga-institution-sites.csv | none | https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tissue-source-site-codes |
| tcga/liu.xlsx | none | https://www.cell.com/cancer-cell/fulltext/S1535-6108(18)30114-4#supplementaryMaterial |
| file name | changes made | retrieved from |
|---|---|---|
| tcga/tcga-cna-part1.txt | none | cbioportal.org (1066 gene list) |
| tcga/tcga-cna-part10.txt | none | cbioportal.org (1066 gene list) |
| tcga/tcga-cna-part11.txt | none | cbioportal.org (1066 gene list) |
| tcga/tcga-cna-part12.txt | none | cbioportal.org (1066 gene list) |
| tcga/tcga-cna-part13.txt | none | cbioportal.org (1066 gene list) |
| tcga/tcga-cna-part14.txt | none | cbioportal.org (1066 gene list) |
| tcga/tcga-cna-part2.txt | none | cbioportal.org (1066 gene list) |
| tcga/tcga-cna-part3.txt | none | cbioportal.org (1066 gene list) |
| tcga/tcga-cna-part4.txt | none | cbioportal.org (1066 gene list) |
| tcga/tcga-cna-part5.txt | none | cbioportal.org (1066 gene list) |
| tcga/tcga-cna-part6.txt | none | cbioportal.org (1066 gene list) |
| tcga/tcga-cna-part7.txt | none | cbioportal.org (1066 gene list) |
| tcga/tcga-cna-part8.txt | none | cbioportal.org (1066 gene list) |
| tcga/tcga-cna-part9.txt | none | cbioportal.org (1066 gene list) |
| tcga/tcga-mutations-part1.txt | none | cbioportal.org (1066 gene list) |
| tcga/tcga-mutations-part10.txt | none | cbioportal.org (1066 gene list) |
| tcga/tcga-mutations-part11.txt | none | cbioportal.org (1066 gene list) |
| tcga/tcga-mutations-part12.txt | none | cbioportal.org (1066 gene list) |
| tcga/tcga-mutations-part13.txt | none | cbioportal.org (1066 gene list) |
| tcga/tcga-mutations-part14.txt | none | cbioportal.org (1066 gene list) |
| tcga/tcga-mutations-part2.txt | none | cbioportal.org (1066 gene list) |
| tcga/tcga-mutations-part3.txt | none | cbioportal.org (1066 gene list) |
| tcga/tcga-mutations-part4.txt | none | cbioportal.org (1066 gene list) |
| tcga/tcga-mutations-part5.txt | none | cbioportal.org (1066 gene list) |
| tcga/tcga-mutations-part6.txt | none | cbioportal.org (1066 gene list) |
| tcga/tcga-mutations-part7.txt | none | cbioportal.org (1066 gene list) |
| tcga/tcga-mutations-part8.txt | none | cbioportal.org (1066 gene list) |
| tcga/tcga-mutations-part9.txt | none | cbioportal.org (1066 gene list) |
| file name | changes made | retrieved from |
|---|---|---|
| cptac/CPTAC_CLINI_Data.xlsx | none | ??? |
| cptac/CPTAC_CLINI_Data.xlsx | none | cbioportal.org |
| cptac/CPTAC_CNA_part1.txt | none | cbioportal.org |
| cptac/CPTAC_CNA_part2.txt | none | cbioportal.org |
| cptac/CPTAC_Mutations_part1.txt | none | cbioportal.org |
| cptac/CPTAC_Mutations_part2.txt | none | cbioportal.org |
| cptac/CPTAC_RNA expression z-scores_part1.txt | none | cbioportal.org |
| cptac/CPTAC_RNA expression z-scores_part2.txt | none | cbioportal.org |
| cptac/CPTAC_sample_matrix_part1.txt | none | cbioportal.org |
| cptac/CPTAC_sample_matrix_part2.txt | none | cbioportal.org |