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tutorial:read_data

Read Data

Example: Read TCGA Breast invasive carcinoma (BRCA) data

Data is downloaded directly from https://gdac.broadinstitute.org/. The results here are in whole or part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga.

brca = TCGACancer('BRCA', download = True)
mRNAseq = brca.mRNAseq
clinical = brca.clinical

All avaialble TCGA cancer

Barcode Cancer full name Version
1 ACC Adrenocortical carcinoma 2016_01_28
2 BLCA Bladder urothelial carcinoma 2016_01_28
3 BRCA Breast invasive carcinoma 2016_01_28
4 CESC Cervical and endocervical cancers 2016_01_28
5 CHOL Cholangiocarcinoma 2016_01_28
6 COAD Colon adenocarcinoma 2016_01_28
7 COADREAD Colorectal adenocarcinoma 2016_01_28
8 DLBC Lymphoid Neoplasm Diffuse Large B-cell Lymphoma 2016_01_28
9 ESCA Esophageal carcinoma 2016_01_28
10 FPPP FFPE Pilot Phase II 2016_01_28
11 GBM Glioblastoma multiforme 2016_01_28
12 GBMLGG Glioma 2016_01_28
13 HNSC Head and Neck squamous cell carcinoma 2016_01_28
14 KICH Kidney Chromophobe 2016_01_28
15 KIPAN Pan-kidney cohort (KICH+KIRC+KIRP) 2016_01_28
16 KIRC Kidney renal clear cell carcinoma 2016_01_28
17 KIRP Kidney renal papillary cell carcinoma 2016_01_28
18 LAML Acute Myeloid Leukemia 2016_01_28
19 LGG Brain Lower Grade Glioma 2016_01_28
20 LIHC Liver hepatocellular carcinoma 2016_01_28
21 LUAD Lung adenocarcinoma 2016_01_28
22 LUSC Lung squamous cell carcinoma 2016_01_28
23 MESO Mesothelioma 2016_01_28
24 OV Ovarian serous cystadenocarcinoma 2016_01_28
25 PAAD Pancreatic adenocarcinoma 2016_01_28
26 PCPG Pheochromocytoma and Paraganglioma 2016_01_28
27 PRAD Prostate adenocarcinoma 2016_01_28
28 READ Rectum adenocarcinoma 2016_01_28
29 SARC Sarcoma 2016_01_28
30 SKCM Skin Cutaneous Melanoma 2016_01_28
31 STAD Stomach adenocarcinoma 2016_01_28
32 STES Stomach and Esophageal carcinoma 2016_01_28
33 TGCT Testicular Germ Cell Tumors 2016_01_28
34 THCA Thyroid carcinoma 2016_01_28
35 THYM Thymoma 2016_01_28
36 UCEC Uterine Corpus Endometrial Carcinoma 2016_01_28
37 UCS Uterine Carcinosarcoma 2016_01_28
38 UVM Uveal Melanoma 2016_01_28
tutorial/read_data.txt · Last modified: 2020/02/12 22:28 by hz9423