├── .gitignore ├── LICENSE.txt ├── README.md ├── data └── test_filter_1.txt ├── notebooks ├── BCGSC microRNA expression.ipynb ├── BRAF-V600 study using CCLE data.ipynb ├── Copy Number segments.ipynb ├── Creating TCGA cohorts -- part 1.ipynb ├── Creating TCGA cohorts -- part 2.ipynb ├── Creating TCGA cohorts -- part 3.ipynb ├── DNA Methylation.ipynb ├── ISB_CGC_Query_of_the_Month_November_2018.ipynb ├── ISB_cgc_bam_slicing_with_pysam.ipynb ├── Protein expression.ipynb ├── README.md ├── RegulomeExplorer_1_Gexpr_CNV.ipynb ├── Somatic Mutations.ipynb ├── TCGA Annotations.ipynb ├── The ISB-CGC open-access TCGA tables in BigQuery.ipynb ├── UNC HiSeq mRNAseq gene expression.ipynb └── isb_cgc_bam_slicing_with_pysam.ipynb └── python ├── README.md ├── createSchema.py ├── createSchemaP3.py ├── gdcCase2Cohort.py ├── isb_auth.py ├── isb_cgc_api_v3_cases.py ├── isb_cgc_api_v3_cohorts.py ├── isb_cgc_api_v3_samples.py ├── isb_cgc_api_v3_users.py ├── isb_curl.py ├── melt_matrix.py ├── pairwise ├── README ├── archive │ ├── bq_filter_file.py │ ├── bq_filter_file_v2.py │ ├── filter_file_test_1.txt │ └── ref_query.txt ├── bqpairwise.py ├── filter_and_annot.py ├── pairwise_fun.py └── tests │ ├── test1 │ ├── filter_file_1.txt │ ├── filter_file_2.txt │ └── filter_file_test_query.sql │ ├── test2 │ ├── filter_file_1.txt │ ├── filter_file_2.txt │ └── filter_file_test_query.sql │ ├── test3 │ ├── filter_file_1.txt │ └── filter_file_2.txt │ ├── test4 │ ├── filter_file_1.txt │ ├── filter_file_2.txt │ └── filter_file_test_query.sql │ └── test5 │ ├── filter_file_1.txt │ └── filter_file_2.txt └── tsv2json.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isb-cgc/examples-Python/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- 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