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TCGA-Assembler 2: Software Pipeline for Automatic Retrieval, Processing, and Integration of TCGA/CPTAC Data


Introduction:

TCGA-Assembler 2 is an open-source, freely available tool that automatically downloads, assembles and processes public The Cancer Genome Atlas (TCGA) data and the Clinical Proteomic Tumor Analysis Consortium (CPTAC) data of TCGA samples. It facilitates downstream data analysis by relieving investigators from the burdens of data preparation. TCGA-Assembler 2 includes two modules. Module A acquires public TCGA data from the Genomic Data Commons (GDC) of the U.S. National Cancer Institute and assembles individual data files into locally stored data tables. It can also acquire mass spectrometry proteomics data of TCGA samples generated by the CPTAC. Module B fulfills various data processing needs to prepare them for downstream analysis. TCGA-Assembler 2 is licensed under the GPL version 3 and can be distributed under GPL version 3.

Contact:

Yitan Zhu: zhuyitan@gmail.com   Yuan Ji: koaeraser@gmail.com

Distribution of TCGA-Assembler Users:

Since its first release in Feb. 2014, TCGA-Assembler has been downloaded and used by 3511 researchers from 69 different countries and regions all over the world. Click here to see the details.

CountryNumber of UsersInstitutions
China1381Tsinghua University, Fudan University, University of Science and Technology of China, Shanghai Jiao Tong University, Beijing Genomics Institute, Ruijin Hospital, Institute of Biophysics (Chinese Academy of Sciences), Shanghai Institutes for Biological Sciences (Chinese Academy of Sciences), China Medical University, Tongji Medical College, Nanjing Medical University, Wuhan university, West China Hospital, Sun Yat-sen University, Capital Medical University, Harbin Medical University, Huazhong University of Science and Technology, CAS-MPG Partner Institute for Computational Biology, University of Science & Technology Beijing, Shanghai University, Jinan University, Central South University, Guangdong Medical College, Third Military Medical University, Guangxi Medical University, Southeast University, ...
United States1122Johns Hopkins University, Harvard University, Stanford University, Princeton University, Massachusetts Institute of Technology, National Cancer Institute, Columbia University, Emory University, Yale University, University of Chicago, University of Michigan, Baylor College of Medicine, The University Of Texas M.D. Anderson Cancer Center, Dana-Farber Cancer Institute, Mayo Clinic, Cleveland Clinic Foundation, Vanderbilt University, The Scripps Research Institute, Mount Sinai School of Medicine, University of Washington, Northwestern University, University of Pennsylvania, Duke University, Brigham and Women's Hospital, Roswell Park Cancer Institute, Albert Einstein College of Medicine, University of Connecticut Health Center, Boston University, University of California at Los Angeles, Georgetown University, Dartmouth College, University of Pittsburgh, Duke Cancer Institute, The Wistar Institute, Moffitt Cancer Institute, Oak Ridge National Lab, University of Washington, Sanofi, ...
Korea, South105Seoul National University, Samsung Medical Center, Samsung Biomedical Research Institute, The Armed Forces Medical Research Institute, Hanyang University, SUNY Korea, ...
India83Assam University, National Institute of Immunology, Institute of Bioinformatics and Applied Biotechnology, Advanced Centre for Treatment Research and Education in Cancer, Centre for Development of Advanced Computing, Datar Genetics Limited, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Positive Bioscience, ...
Taiwan76National Yang-ming University, Taipei Medical University, Academia Sinica Institute of Biological Chemistry, Tri-Service General Hospital, National Taiwan University, Chang Gung Bioinformatics Center, Wan Fang Hospital, Chang Gung Hospital, ...
Canada68Mount Sinai Hospital, University Health Network, Ontario Institute for Cancer Research, The Hospital for Sick Children, The INRS-Institut Armand-Frappier Research Centre, Princess Margaret Cancer Centre, McGill University, The University of British Columbia, Ottawa Hospital Research Institute, University of Guelph, ...
United Kingdom66Oxford University, University of Cambridge, European Bioinformatics Institute, Welcome Trust Sanger Institute, Institute of Cancer Research, Cancer Research UK, University College London, King's College London, Thomson Reuters, Imperial College London, Queen's University Belfast, University of Dundee, University of Sheffield, Jenner Institute, ...
Germany52The German Cancer Research Center, Heidelberg University, Technical University of Munich, University Medical Center Hamburg-Eppendorf, University of Münster, German Research Center for Environmental Health, University of Applied Sciences Koblenz, Bayer HealthCare AG, Cellzome AG, University of Kiel, Ludwig Maximilian University of Munich, University of Cologne, ...
Italy49European Institute of Oncology, University of Pavia, University of Turin, Biomedical University of Rome, University of Rome Tor Vergata, Fondazione Edo ed Elvo Tempia Valenta, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori, Biogem Institute, ...
Denmark40University of Copenhagen, Aarhus University, ...
Spain39University of Málaga, Spanish National Cancer Research Center, Centre of Studies and Technical Research, Institute of Predictive and Personalized Medicine of Cancer, Navarra-Biomed, University of Navarra, Center for Research in Environmental Epidemiology, Vall d'Hebron Institute of Oncology, Príncipe Felipe Research Center, National Center for Genome Analysis, ...
Japan38Kyushu University, Hamamatsu University School of Medicine, ...
Australia38The University of Sydney, Royal Melbourne Hospital, The University of Queensland, University of Melbourne, The Walter and Eliza Hall Insitute of Medical Research, ...
France36Centre for Cancer Research in Lyon, Centre Léon-Bérard, National Institute of Health and Medical Research, European Institute for Systems Biology and Medicine, ...
Netherlands34University of Amsterdam, Delft University of Technology, Leiden University Medical Center, Academic Medical Center, Utrecht University, VU University Amsterdam, Radboud university medical center, ...
Sweden29Chalmers University of Technology, Karolinska Institute, Lund University, Umea University, ...
Hong Kong29The Chinese University of Hong Kong, The University of Hong Kong, ...
Singapore27Cancer Science Institute, Duke-NUS Graduate Medical School, Genome Institute of Singapore, National University of Singapore, Bioinformatics Institute (BII), ...
Brazil22Federal University of Paraiba, Universidade Federal de Mato Grosso do Sul, Universidade de São Paulo, ...
Israel20Ben-Gurion University of the Negev, Tel Aviv Sourasky medical center, Hebrew University of Jerusalem, ...
Iran17University of Tehran, Iran Blood Transfusion Organization, ...
Turkey16Bilkent University, Dokuz Eylul University, Koc University, Karadeniz Technical University, ...
Finland15University of Turku, University of Helsinki, ...
Norway11University of Bergen, University of Oslo, ...
Argentina11University of Buenos Aires, Institute of Experimental Medicine and Biology of Cuyo, ...
Russia10Ulyanovsk State University, ITMO University, ...
Austria9Medical University of Graz, ...
Belgium9iTeos Therapeutics, ...
Switzerland8Novartis AG, University Hospital Zurich, SIB Swiss Institute of Bioinformatics, ...
Qatar6Carnegie Mellon University in Qatar, Sidra Medical and Research Center
Portugal6Ipatimup Institute of Molecular Pathology and Immunology of the University of Porto, ...
Poland6Wroclaw Medical University, Selvita S.A., ...
Chile5Pontifical Catholic University of Chile, ...
Greece5University of Patras, Foundation for Research & Technology - Hellas (FORTH), ...
Luxembourg4Luxembourg Centre for Systems Biomedicine, ...
Mexico4The National Institute of Genomic Medicine, ...
Pakistan3COMSATS Institute of Information Technology, ...
Hungary3Eötvös Loránd University, ...
Lithuania2Lithuanian University of Health Sciences, ...
Romania2Solutions of Artificial Intelligence Applications (SAIA), ...
Uruguay1Biological Research Institute Clemente Estable, ...
Czech Republic1Czech Technical University in Prague, ...
Serbia and Montenegro1Seven Bridges Genomics, Inc, ...
South Africa1University of Cape Town, ...
Costa Rica1University of Costa Rica, ...

Please cite:

Recent News:

Summary of TCGA data that can be retrieved using TCGA-Assembler 2 (accurate as of April 24, 2017)

Cancer type Number of patient samples (including both tumor and normal tissue samples) Number of patients with clinical information
Somatic mutation Copy number alternation DNA methylation Gene expression miRNA expression Protein expression (RPPA) Protein expression (iTRAQ)
Adrenocortical carcinoma (ACC) 92 180 80 79 80 46 92
Bladder urothelial carcinoma (BLCA) 413 806 434 427 429 344 412
Breast invasive carcinoma (BRCA) 1092 2207 1228 1215 1189 937 105 1097
Cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) 307 586 312 309 312 173 307
Cholangiocarcinoma (CHOL) 36 85 45 45 45 30 45
Colon adenocarcinoma (COAD) 423 920 535 481 455 362 60 459
Lymphoid neoplasm diffuse large B-cell lymphoma (DLBC) 48 96 48 48 47 33 48
Esophageal carcinoma (ESCA) 186 373 202 196 198 126 185
Glioblastoma multiforme (GBM) 409 1110 437 172 5 244 596
Head and neck squamous cell carcinoma (HNSC) 528 1090 580 566 569 357 528
Kidney chromophobe (KICH) 66 132 66 91 91 63 113
Kidney renal clear cell carcinoma (KIRC) 504 1059 895 607 588 478 537
Kidney renal papillary cell carcinoma (KIRP) 290 593 342 323 326 216 291
Acute myeloid leukemia (LAML) 201 392 194 173 188 0 200
Brain lower grade glioma (LGG) 530 1015 530 530 526 435 515
Liver hepatocellular carcinoma (LIHC) 377 760 429 423 424 184 377
Lung adenocarcinoma (LUAD) 572 1095 636 576 561 365 522
Lung squamous cell carcinoma (LUSC) 493 1035 572 555 523 328 504
Mesothelioma (MESO) 83 173 87 87 87 63 87
Ovarian serous cystadenocarcinoma (OV) 583 1172 622 577 493 436 174 587
Pancreatic adenocarcinoma (PAAD) 186 368 195 183 183 123 185
Pheochromocytoma and paraganglioma (PCPG) 184 360 187 187 187 82 179
Prostate adenocarcinoma (PRAD) 499 1031 549 550 547 352 500
Rectum adenocarcinoma (READ) 157 316 178 173 165 132 30 170
Sarcoma (SARC) 262 516 269 265 263 226 261
Skin cutaneous melanoma (SKCM) 472 938 475 473 452 355 470
Stomach adenocarcinoma (STAD) 441 906 470 450 477 357 443
Testicular germ cell tumors (TGCT) 156 304 156 156 156 122 134
Thyroid carcinoma (THCA) 504 1020 571 572 573 374 507
Thymoma (THYM) 123 248 126 122 126 90 124
Uterine corpus endometrial carcinoma (UCEC) 545 1094 595 253 572 440 548
Uterine carcinosarcoma (UCS) 57 110 57 57 57 47 57
Uveal melanoma (UVM) 80 160 80 80 80 12 80
Total 10899 22250 12182 11001 10974 7932 369 11160