├── .BBSoptions ├── .Rbuildignore ├── .github └── workflows │ ├── pr_check.yml │ ├── test_conda_build.yml │ └── update_api.yml ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── NEWS.md ├── R ├── cBioDataPack.R ├── cBioPortal-class.R ├── cBioPortal.R ├── cBioPortalData-pkg.R ├── cBioPortalData.R ├── cache.R └── utils.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── inst ├── CITATION ├── REFERENCES.bib ├── docker │ ├── Dockerfile │ ├── environment.yml │ ├── pkg │ │ └── Dockerfile │ └── scripts │ │ └── test.sh ├── extdata │ ├── api │ │ ├── api_build.json │ │ └── err_api_info.json │ ├── metadata_table.rds │ └── pack │ │ ├── err_pack_info.json │ │ └── pack_build.json ├── scripts │ ├── allclin_cbio.R │ ├── buildStudies │ │ ├── api_studies.R │ │ ├── checkBuildFiles.R │ │ └── pack_studies.R │ ├── gdcMAE.R │ ├── headermap.R │ ├── runDatasets.R │ ├── testDataPack.R │ ├── testStudyComplete.R │ └── update_api-docs.R └── service │ └── cBioPortal │ └── api.json ├── longtests ├── testthat.R └── 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