Running examples in 'cgdsr-Ex.R' failed
The error most likely occurred in:

> ### Name: cgdsr-getCancerStudies
> ### Title: Get available cancer studies available in CGDS
> ### Aliases: cgdsr-getCancerStudies getCancerStudies getCancerStudies.CGDS
> 
> ### ** Examples
> 
> # Create CGDS object
> mycgds = CGDS("http://www.cbioportal.org/")
> 
> getCancerStudies(mycgds)
                     cancer_study_id
1                      paac_jhu_2014
2                      laml_tcga_pub
3                          laml_tcga
4                      acyc_fmi_2014
5                      acyc_mda_2015
6                    acyc_mskcc_2013
7                   acyc_sanger_2013
8                    acbc_mskcc_2015
9                           acc_tcga
10                    ampca_bcm_2016
11             blca_mskcc_solit_2014
12             blca_mskcc_solit_2012
13      blca_plasmacytoid_mskcc_2016
14                          blca_bgi
15           blca_dfarber_mskcc_2014
16                     blca_tcga_pub
17                         blca_tcga
18                          lgg_tcga
19                     brca_metabric
20                        brca_bccrc
21                        brca_broad
22                       brca_sanger
23                 brca_tcga_pub2015
24                     brca_tcga_pub
25                         brca_tcga
26         brca_bccrc_xenograft_2014
27               cellline_ccle_broad
28                         cesc_tcga
29                    chol_nccs_2013
30                     chol_nus_2012
31                         chol_tcga
32                   lcll_broad_2013
33                    cll_iuopa_2015
34                 ccrcc_utokyo_2013
35                coadread_dfci_2016
36                coadread_genentech
37                 coadread_tcga_pub
38                     coadread_tcga
39                    coadread_mskcc
40                ctcl_columbia_2015
41                 cscc_dfarber_2015
42                     pact_jhu_2011
43                   desm_broad_2015
44                   dlbc_broad_2012
45                        esca_broad
46                         esca_tcga
47                         escc_icgc
48                    escc_ucla_2014
49                   es_iocurie_2014
50                 gbc_shanghai_2014
51                   egc_tmucih_2015
52                  nsclc_unito_2016
53                    prad_cpcg_2017
54                      gct_msk_2016
55                  gbm_tcga_pub2013
56                      gbm_tcga_pub
57                          gbm_tcga
58                        hnsc_broad
59                          hnsc_jhu
60                     hnsc_tcga_pub
61                         hnsc_tcga
62               liad_inserm_fr_2014
63                hcc_inserm_fr_2015
64                   all_stjude_2013
65                   all_stjude_2015
66               panet_shanghai_2013
67                     chol_jhu_2013
68                     kich_tcga_pub
69                         kich_tcga
70                          kirc_bgi
71                     kirc_tcga_pub
72                         kirc_tcga
73                         kirp_tcga
74                      lihc_amc_prv
75                        lihc_riken
76                         lihc_tcga
77                     lgg_ucsf_2014
78                        luad_broad
79                   luad_mskcc_2015
80                     luad_tcga_pub
81                         luad_tcga
82                          luad_tsp
83                     lusc_tcga_pub
84                         lusc_tcga
85                         dlbc_tcga
86                   msk_impact_2017
87                       mpnst_mskcc
88                   plmeso_nyu_2015
89                  mcl_idibips_2013
90                    mbl_broad_2012
91                          mbl_icgc
92                          mbl_pcgp
93                 mbl_sickkids_2016
94                skcm_broad_dfarber
95                   lgggbm_tcga_pub
96                         meso_tcga
97                    prad_su2c_2015
98                          mm_broad
99                    ccrcc_irc_2014
100                    brca_igr_2015
101                   mds_tokyo_2011
102                   cellline_nci60
103                  npc_nusingapore
104                     nbl_amc_2012
105                nbl_ucologne_2015
106                    nepc_wcm_2016
107             hnsc_mdanderson_2013
108                      ov_tcga_pub
109                          ov_tcga
110            nsclc_tcga_broad_2016
111                        paad_icgc
112                paad_qcmg_uq_2016
113                        paad_tcga
114                   paad_utsw_2015
115                   panet_jhu_2011
116                    thca_tcga_pub
117            es_dfarber_broad_2014
118                        pcpg_tcga
119               thyroid_mskcc_2016
120                  pcnsl_mayo_2015
121                  prad_broad_2013
122                       prad_broad
123                       prad_fhcrc
124                       prad_mskcc
125                    prad_tcga_pub
126                        prad_tcga
127                  prad_mskcc_2014
128 prad_mskcc_cheny1_organoids_2014
129                        prad_mich
130                   hnc_mskcc_2016
131            nccrcc_genentech_2014
132                     rms_nih_2014
133                       sarc_mskcc
134                        sarc_tcga
135                       skcm_broad
136                        skcm_tcga
137                        skcm_yale
138                       scco_mskcc
139                       sclc_clcgp
140                         sclc_jhu
141               sclc_ucologne_2015
142            stad_pfizer_uhongkong
143                    stad_tcga_pub
144                        stad_tcga
145                      stad_utokyo
146                   stad_uhongkong
147                    stes_tcga_pub
148                        tgct_tcga
149                     tet_nci_2014
150                        thym_tcga
151                        thca_tcga
152                  urcc_mskcc_2016
153                     ucs_jhu_2014
154                         ucs_tcga
155                    ucec_tcga_pub
156                        ucec_tcga
157                         uvm_tcga
158                panet_arcnet_2017
159        past_dkfz_heidelberg_2013
                                                                                               name
1                              Acinar Cell Carcinoma of the Pancreas (Johns Hopkins, J Pathol 2014)
2                                                          Acute Myeloid Leukemia (TCGA, NEJM 2013)
3                                                        Acute Myeloid Leukemia (TCGA, Provisional)
4                                             Adenoid Cystic Carcinoma (FMI, Am J Surg Pathl. 2014)
5                                              Adenoid Cystic Carcinoma (MDA, Clin Cancer Res 2015)
6                                                  Adenoid Cystic Carcinoma (MSKCC, Nat Genet 2013)
7                                                   Adenoid Cystic Carcinoma (Sanger/MDA, JCI 2013)
8                                    Adenoid Cystic Carcinoma of the Breast (MSKCC, J Pathol. 2015)
9                                                      Adrenocortical Carcinoma (TCGA, Provisional)
10                              Ampullary Carcinoma (Baylor College of Medicine, Cell Reports 2016)
11                                                            Bladder Cancer (MSKCC, Eur Urol 2014)
12                                                                 Bladder Cancer (MSKCC, JCO 2013)
13                                     Bladder Cancer, Plasmacytoid Variant (MSKCC, Nat Genet 2016)
14                                               Bladder Urothelial Carcinoma (BGI, Nat Genet 2013)
15                           Bladder Urothelial Carcinoma (Dana Farber & MSKCC, Cancer Discov 2014)
16                                                 Bladder Urothelial Carcinoma (TCGA, Nature 2014)
17                                                 Bladder Urothelial Carcinoma (TCGA, Provisional)
18                                                     Brain Lower Grade Glioma (TCGA, Provisional)
19                                          Breast Cancer (METABRIC, Nature 2012 & Nat Commun 2016)
20                                        Breast Invasive Carcinoma (British Columbia, Nature 2012)
21                                                   Breast Invasive Carcinoma (Broad, Nature 2012)
22                                                  Breast Invasive Carcinoma (Sanger, Nature 2012)
23                                                      Breast Invasive Carcinoma (TCGA, Cell 2015)
24                                                    Breast Invasive Carcinoma (TCGA, Nature 2012)
25                                                    Breast Invasive Carcinoma (TCGA, Provisional)
26                                 Breast cancer patient xenografts (British Columbia, Nature 2014)
27                                      Cancer Cell Line Encyclopedia (Novartis/Broad, Nature 2012)
28             Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (TCGA, Provisional)
29                         Cholangiocarcinoma (National Cancer Centre of Singapore, Nat Genet 2013)
30                            Cholangiocarcinoma (National University of Singapore, Nat Genet 2012)
31                                                           Cholangiocarcinoma (TCGA, Provisional)
32                                                  Chronic Lymphocytic Leukemia (Broad, Cell 2013)
33                                                Chronic Lymphocytic Leukemia (IUOPA, Nature 2015)
34                                        Clear Cell Renal Cell Carcinoma (U Tokyo, Nat Genet 2013)
35                                              Colorectal Adenocarcinoma (DFCI, Cell Reports 2016)
36                                               Colorectal Adenocarcinoma (Genentech, Nature 2012)
37                                                    Colorectal Adenocarcinoma (TCGA, Nature 2012)
38                                                    Colorectal Adenocarcinoma (TCGA, Provisional)
39                                     Colorectal Adenocarcinoma Triplets (MSKCC, Genome Biol 2014)
40                                           Cutaneous T Cell Lymphoma (Columbia U, Nat Genet 2015)
41                                   Cutaneous squamous cell carcinoma (DFCI, Clin Cancer Res 2015)
42                                           Cystic Tumor of the Pancreas (Johns Hopkins, PNAS 2011
43                                          Desmoplastic Melanoma (Broad Institute, Nat Genet 2015)
44                                                 Diffuse Large B-Cell Lymphoma (Broad, PNAS 2012)
45                                                Esophageal Adenocarcinoma (Broad, Nat Genet 2013)
46                                                         Esophageal Carcinoma (TCGA, Provisional)
47                                           Esophageal Squamous Cell Carcinoma (ICGC, Nature 2014)
48                                        Esophageal Squamous Cell Carcinoma (UCLA, Nat Genet 2014)
49                                               Ewing Sarcoma (Institut Cuire, Cancer Discov 2014)
50                                                 Gallbladder Carcinoma (Shanghai, Nat Genet 2014)
51                                                       Gastric Adenocarcinoma (TMUCIH, PNAS 2015)
52  Genetic Characterization of NSCLC young adult patients ( University of Turin, Lung Cancer 2016)
53                             Genomic Hallmarks of Prostate Adenocarcinoma (CPC-GENE, Nature 2017)
54                      Genomic Profile of Patients with Advanced Germ Cell Tumors (MSK, JCO 2016).
55                                                                   Glioblastoma (TCGA, Cell 2013)
56                                                                 Glioblastoma (TCGA, Nature 2008)
57                                                      Glioblastoma Multiforme (TCGA, Provisional)
58                                      Head and Neck Squamous Cell Carcinoma (Broad, Science 2011)
59                              Head and Neck Squamous Cell Carcinoma (Johns Hopkins, Science 2011)
60                                        Head and Neck Squamous Cell Carcinoma (TCGA, Nature 2015)
61                                        Head and Neck Squamous Cell Carcinoma (TCGA, Provisional)
62                                                Hepatocellular Adenoma (Inserm, Cancer Cell 2014)
63                                               Hepatocellular Carcinomas (Inserm, Nat Genet 2015)
64                                    Hypodiploid Acute Lymphoid Leukemia (St Jude, Nat Genet 2013)
65                     Infant MLL-Rearranged Acute Lymphoblastic Leukemia (St Jude, Nat Genet 2015)
66                                                           Insulinoma (Shanghai, Nat Commun 2013)
67                       Intrahepatic Cholangiocarcinoma (Johns Hopkins University, Nat Genet 2013)
68                                                      Kidney Chromophobe (TCGA, Cancer Cell 2014)
69                                                           Kidney Chromophobe (TCGA, Provisional)
70                                          Kidney Renal Clear Cell Carcinoma (BGI, Nat Genet 2012)
71                                            Kidney Renal Clear Cell Carcinoma (TCGA, Nature 2013)
72                                            Kidney Renal Clear Cell Carcinoma (TCGA, Provisional)
73                                        Kidney Renal Papillary Cell Carcinoma (TCGA, Provisional)
74                                            Liver Hepatocellular Carcinoma (AMC, Hepatology 2014)
75                                           Liver Hepatocellular Carcinoma (RIKEN, Nat Genet 2012)
76                                               Liver Hepatocellular Carcinoma (TCGA, Provisional)
77                                                           Low-Grade Gliomas (UCSF, Science 2014)
78                                                           Lung Adenocarcinoma (Broad, Cell 2012)
79                                                                 Lung Adenocarcinoma (MSKCC 2015)
80                                                          Lung Adenocarcinoma (TCGA, Nature 2014)
81                                                          Lung Adenocarcinoma (TCGA, Provisional)
82                                                           Lung Adenocarcinoma (TSP, Nature 2008)
83                                                 Lung Squamous Cell Carcinoma (TCGA, Nature 2012)
84                                                 Lung Squamous Cell Carcinoma (TCGA, Provisional)
85                              Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (TCGA, Provisional)
86                                      MSK-IMPACT Clinical Sequencing Cohort (MSKCC, Nat Med 2017)
87                                  Malignant Peripheral Nerve Sheath Tumor (MSKCC, Nat Genet 2014)
88                                            Malignant Pleural Mesothelioma (NYU, Cancer Res 2015)
89                                                        Mantle Cell Lymphoma (IDIBIPS, PNAS 2013)
90                                                             Medulloblastoma (Broad, Nature 2012)
91                                                              Medulloblastoma (ICGC, Nature 2012)
92                                                              Medulloblastoma (PCGP, Nature 2012)
93                                                          Medulloblastoma (Sickkids, Nature 2016)
94                                                        Melanoma (Broad/Dana Farber, Nature 2012)
95                                                   Merged Cohort of LGG and GBM (TCGA, Cell 2016)
96                                                                 Mesothelioma (TCGA, Provisional)
97                     Metastatic Prostate Cancer, SU2C/PCF Dream Team (Robinson et al., Cell 2015)
98                                                       Multiple Myeloma (Broad, Cancer Cell 2014)
99                 Multiregion Sequencing of Clear Cell Renal Cell Carcinoma (IRC, Nat Genet 2014).
100                                  Mutational profiles of metastatic breast cancer (France, 2016)
101                                                             Myelodysplasia (Tokyo, Nature 2011)
102                                                       NCI-60 Cell Lines (NCI, Cancer Res. 2012)
103                                            Nasopharyngeal Carcinoma (Singapore, Nat Genet 2014)
104                                                      Neuroblastoma (AMC Amsterdam, Nature 2012)
105                                                           Neuroblastoma (Broad, Nat Genet 2013)
106                                      Neuroendocrine Prostate Cancer (Trento/Cornell/Broad 2016)
107                                  Oral Squamous Cell Carcinoma (MD Anderson, Cancer Discov 2013)
108                                           Ovarian Serous Cystadenocarcinoma (TCGA, Nature 2011)
109                                           Ovarian Serous Cystadenocarcinoma (TCGA, Provisional)
110                                                          Pan-Lung Cancer (TCGA, Nat Genet 2016)
111                                                   Pancreatic Adenocarcinoma (ICGC, Nature 2012)
112                                                   Pancreatic Adenocarcinoma (QCMG, Nature 2016)
113                                                   Pancreatic Adenocarcinoma (TCGA, Provisional)
114                                                       Pancreatic Cancer (UTSW, Nat Commun 2015)
115                       Pancreatic Neuroendocrine Tumors (Johns Hopkins University, Science 2011)
116                                                   Papillary Thyroid Carcinoma (TCGA, Cell 2014)
117                                              Pediatric Ewing Sarcoma (DFCI, Cancer Discov 2014)
118                                          Pheochromocytoma and Paraganglioma (TCGA, Provisional)
119                          Poorly-Differentiated and Anaplastic Thyroid Cancers (MSKCC, JCI 2016)
120                     Primary Central Nervous System Lymphoma (Mayo Clinic, Clin Cancer Res 2015)
121                                              Prostate Adenocarcinoma (Broad/Cornell, Cell 2013)
122                                         Prostate Adenocarcinoma (Broad/Cornell, Nat Genet 2012)
123                                     Prostate Adenocarcinoma (Fred Hutchinson CRC, Nat Med 2016)
124                                               Prostate Adenocarcinoma (MSKCC, Cancer Cell 2010)
125                                                       Prostate Adenocarcinoma (TCGA, Cell 2015)
126                                                     Prostate Adenocarcinoma (TCGA, Provisional)
127                                            Prostate Adenocarcinoma CNA study (MSKCC, PNAS 2014)
128                                            Prostate Adenocarcinoma Organoids (MSKCC, Cell 2014)
129                                     Prostate Adenocarcinoma, Metastatic (Michigan, Nature 2012)
130                               Recurrent and Metastatic Head & Neck Cancer (JAMA Oncology, 2016)
131                                      Renal Non-Clear Cell Carcinoma (Genentech, Nat Genet 2014)
132                                                      Rhabdomyosarcoma (NIH, Cancer Discov 2014)
133                                                           Sarcoma (MSKCC/Broad, Nat Genet 2010)
134                                                                     Sarcoma (TCGA, Provisional)
135                                                      Skin Cutaneous Melanoma (Broad, Cell 2012)
136                                                     Skin Cutaneous Melanoma (TCGA, Provisional)
137                                                  Skin Cutaneous Melanoma (Yale, Nat Genet 2012)
138                                       Small Cell Carcinoma of the Ovary (MSKCC, Nat Genet 2014)
139                                                  Small Cell Lung Cancer (CLCGP, Nat Genet 2012)
140                                          Small Cell Lung Cancer (Johns Hopkins, Nat Genet 2012)
141                                                 Small Cell Lung Cancer (U Cologne, Nature 2015)
142                                         Stomach Adenocarcinoma (Pfizer and UHK, Nat Genet 2014)
143                                                      Stomach Adenocarcinoma (TCGA, Nature 2014)
144                                                      Stomach Adenocarcinoma (TCGA, Provisional)
145                                                Stomach Adenocarcinoma (U Tokyo, Nat Genet 2014)
146                                                    Stomach Adenocarcinoma (UHK, Nat Genet 2011)
147                                     TCGA data for Esophagus-Stomach Cancers (TCGA, Nature 2017)
148                                                 Testicular Germ Cell Cancer (TCGA, Provisional)
149                                                  Thymic Epithelial Tumors (NCI, Nat Genet 2014)
150                                                                     Thymoma (TCGA, Provisional)
151                                                           Thyroid Carcinoma (TCGA, Provisional)
152                                                  Unclassified Renal Cell Carcinoma (MSKCC 2016)
153                              Uterine Carcinosarcoma (Johns Hopkins University, Nat Commun 2014)
154                                                      Uterine Carcinosarcoma (TCGA, Provisional)
155                                        Uterine Corpus Endometrial Carcinoma (TCGA, Nature 2013)
156                                        Uterine Corpus Endometrial Carcinoma (TCGA, Provisional)
157                                                              Uveal Melanoma (TCGA, Provisional)
158                      Whole-Genome Sequencing of Pancreatic Neuroendocrine Tumors (Nature, 2017)
159                      Whole-genome sequencing of pilocytic astrocytomasatic (Nat Genetics, 2013)
                                                                                                                                                                                                                                                                                                                                    description
1                                                                                                                                                                                                                        Mutation data from whole exome sequencing of 23 surgically resected pancreatic carcinomas with acinar differentiation.
2                                                                                                                                 TCGA Acute Myeloid Leukemia, analysis of 200 adult cases; raw data at the <A HREF="https://tcga-data.nci.nih.gov/tcga/tcgaCancerDetails.jsp?diseaseType=LAML&diseaseName=Acute%20Myeloid%20Leukemia">NCI</A>.
3                                                                                                                                                                                                                                                TCGA Acute Myeloid Leukemia; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
4                                                                                                                                                                                                                                                                                        Comprehensive genomic profiling of 28 metastatic ACCs.
5                                                                                                                                                                                                                                                    WGS of 21 salivary ACCs and targeted molecular analyses of a validation set (81 patients).
6                                                                                                                                                                                                                                                                                        Exome profiling of 60 adenoid cystic carcinoma samples
7                                                                                                                                                                                                                                                                                                            Whole exome sequencing of 24 ACCs.
8                                                                                                                                                                                                                                                                                                    Whole exome sequencing of 12 breast AdCCs.
9                                                                                                                                                                                                                                              TCGA Adrenocortical Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
10                                                     Mutation data from exome sequencing analysis of 160 cancers arising in the periampullary region, 62 of these clearly arising from either the bile duct (n = 44) or the duodenum (n = 18) and 98 for which the epithelium of origin could not be clearly defined morphologically (AMPCA).
11                                                                                                                                                                     Genomic Predictors of Survival in Patients with High-grade Urothelial Carcinoma of the Bladder. Targeted sequencing of 109 tumor samples (MSKCC, European Urology 2014).
12                                                                                                                                                                                                           Comprehensive profiling of 97 bladder cancer samples, including targeted sequencing of 15 cancer genes. Iyer et al., JCO in press.
13                                                                                                                                                                                                                                            Genomic profiling of plasmacytoid-variant (signet ring cell) tumors of the bladder, published set
14                                                                                                                                                                                                                                                            Exome and whole-genome sequencing of 99 bladder cancer samples. Generated by BGI.
15                                                                                                                                                                                                                                                              Whole exome sequencing of 50 patients with muscle invasive urothelial carcinoma
16                                                                                                                                                                                                                                                                            TCGA Bladder Cancer, containing 131 samples; raw data at the NCI.
17                                                                                                                                                                                                                                         TCGA Bladder Urothelial Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
18                                                                                                                                                                                                                                             TCGA Brain Lower Grade Glioma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
19                                                                                                                                                                                                         The genomic profiles (somatic mutations [targeted sequencing], copy number alterations, and gene expression) of 2509 breast cancers.
20                                                                                                                                                                                                                               Comprehensive profiling of 65 breast cancer samples. Generated by the British Columbia Cancer Research Centre.
21                                                                                                                                                                                                                                                      Comprehensive profiling of 103 breast cancer samples. Generated by the Broad Institute.
22                                                                                                                                                                                                                                                     Comprehensive profiling of 100 breast cancer samples. Generated by the Sanger Institute.
23                                                                                                                                                                                                     <a href="http://cancergenome.nih.gov/">The Cancer Genome Atlas (TCGA)</a> Breast Invasive Carcinoma project. 817 cases (TCGA Cell 2015).
24                                                                                   <a href="http://cancergenome.nih.gov/">The Cancer Genome Atlas (TCGA)</a> Breast Invasive Carcinoma project. 825 cases.<br><i>Nature 2012.</i> <a href="https://tcga-data.nci.nih.gov/docs/publications/brca_2012/">Raw data via the TCGA Data Portal</a>.
25                                                                                                                                                                                                                                            TCGA Breast Invasive Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
26                                                                                                                                                                                                                                                                              Dynamics of genomic clones in breast cancer patient xenografts.
27                                                                                                                            Cancer Cell Line Encyclopedia from the Broad Institute and Novartis, containing 883 samples; raw data at the <A HREF="http://www.broadinstitute.org/ccle/data/browseData?conversationPropagation=begin">CCLE</A>.
28                                                                                                                                                                                                     TCGA Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
29                                                                                                                                                                                                                 Exome sequencing of 15 cholangiocarcinoma cases from the National Cancer Centre of Singapore to study the somatic mutations.
30                                                                                                                                                                                                            Exome Sequencing for Opisthorchis viverrini-related cholangiocarcinoma in 8 O.viverrini-related tumors and matched normal tissue.
31                                                                                                                                                                                                                                                   TCGA Cholangiocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
32                                                                                                                                                                                                                                                                       Exome sequencing of 160 CLL samples. Generated by the Broad Institute.
33                                                                                                                                                                                                                                  Mutation data from whole-genome or whole-exome sequencing (WGS/WXS) of 428 CLL, 54 MBL, and 24 SLL samples.
34                                                                                                                                                                                                                                Mutation data from whole genome and/or whole exome sequencing of 106 clear-cell renal cell carcinoma samples.
35                                                                                                                                                                                                                                                         Whole-exome sequencing of 619 colorectal cancers with clinicopathologic annotations.
36                                                                                                                                                                                                                                                                  Comprehensive profiling of 72 colon cancer samples. Generated by Genentech.
37                                                                                                 <a href="http://cancergenome.nih.gov/">The Cancer Genome Atlas (TCGA)</a> Colorectal Cancer project. <br><i>Nature 2012.</i> <a href="https://tcga-data.nci.nih.gov/docs/publications/coadread_2012/">Raw data via the TCGA Data Portal</a>.
38                                                                                                                                                                                                                                            TCGA Colorectal Adenocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
39                                                                                                                                                                                             Colon Trios data from 69 Patients each with a  primary and metastatic tumor. (Primary / Met) (David Solit / Evi Vakiani / Michael Berger, MSKCC)
40                                                                                                                                                                                Whole-Exome Sequencing (WXS) of tumor-normal sample pairs from 25 patients with Sezary Syndrome and 17 patients with other Cutaneous T Cell Lymphoma (CTCLs).
41                                                                                                                                                                                                                                           Targeted sequencing of 504 cancer-associated genes in 29 cutaneous squamous cell carcinoma samples
42                                                                                                   Whole-exome sequencing of major neoplastic cyst types of the pancreas: 8 serous cystadenomas (SCAs), 8 intraductal papillary mucinous neoplasms (IPMNs), 8 mucinous cystic neoplasms (MCNs), and 8 solid pseudopapillary neoplasms (SPNs).
43                                                                                                                                                                                                                                                          Mutation data from Exome/Whole Genome sequencing of 20 desmoplastic melanoma cases.
44                                                                                                                                                                                                                                                                                                  Whole exome sequencing of 58 DLBCL samples.
45                                                                                                                                                                                                                                                   Comprehensive profiling of 149 esophageal adenocarcinoma samples from the Broad Institute.
46                                                                                                                                                                                                                                                TCGA Esophageal Carcinoma ; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
47                                                                                                                                                                                                                                                             WGS and WES of 88 esophageal squamous cell carcinoma samples. Generated by ICGC.
48                                                                                                                                                                                                                    Whole exome sequencing (WXS) or targeted deep sequencing (TDS) of 139 paired esophageal squamous cell carcinoma patients.
49                                                                                                                                                            Mutation data from whole-genome sequencing of 112 Ewing sarcoma samples and matched germ line DNA. <a href="http://cancerdiscovery.aacrjournals.org/content/4/11/1342/suppl/DC1">
50                                                                                                                                                                                                                                             Mutation data from whole exome sequencing of 32 gallbladder carcinoma tumors with paired normals
51                                                                                                                                                                                                                                          Whole-exome sequencing on 78 Gastric Adenocarcinoma of differing histologies and anatomic locations
52                                                                                                                                                                                                                                        The retrospective study using NGS approach for genetic characterization of NSCLC young adult patients
53                                                                                                                                                                                                              Comprehensive genomic profiling of 477 Prostate Adenocarcinoma samples from CPC-GENE and public data sets, including TCGA-PRAD.
54                                                                                                                                                                                                                                                                                      Comprehensive profiling of 180 germ cell tumor samples.
55                                                                                                                                                      <a href="http://cancergenome.nih.gov/">The Cancer Genome Atlas (TCGA)</a> Glioblastoma project.<br> <a href="http://tcga-data.nci.nih.gov/tcga/">Raw data via the TCGA Data Portal</a>.
56                                                                                             <a href="http://cancergenome.nih.gov/">The Cancer Genome Atlas (TCGA)</a> Glioblastoma project. 206 primary glioblastoma samples.<br> <a href="https://tcga-data.nci.nih.gov/docs/publications/gbm_2008/">Raw data via the TCGA Data Portal</a>.
57                                                                                                                                                                                                                                              TCGA Glioblastoma Multiforme; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
58                                                                                                                                                                                                                                        Comprehensive profiling of 74 head and neck squamous cell carcinoma samples from the Broad Institute.
59                                                                                                                                                                                                                                              Comprehensive profiling of 32 head and neck squamous cell carcinoma samples from Johns Hopkins.
60                                                                                                           TCGA Head and Neck Squamous Cell Carcinoma, containing 279 samples; raw data at the <A HREF="https://tcga-data.nci.nih.gov/tcga/tcgaCancerDetails.jsp?diseaseType=HNSC&diseaseName=Head and Neck Squamous Cell Carcinoma">NCI</A>.
61                                                                                                                                                                                                                                TCGA Head and Neck Squamous Cell Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
62                                                                                                                                                                                                                                            Mutation data from whole-exome sequencing (WXS) of 46 liver tumor and corresponding nontumor DNA.
63                                                                                                                                                                                                  Mutation data from whole-exome sequencing (WXS) of 243 liver tumors identified mutational signatures associated with specific risk factors.
64                                                                                                                                                                                                                                                                                                          Exome sequencing of 44 ALL samples.
65                                                                                                                                                                                                                                     Whole genome sequencing (WGS) of 22 infant MLL-rearranged acute lymphoblastic leukemia (MLL-R ALL) cases
66                                                                                                                                                                                               Whole exome sequencing of 10 benign insulinoma tumors. <A HREF="http://www.nature.com/ncomms/2013/131210/ncomms3810/extref/ncomms3810-s1.pdf">
67                                                                                                                                                                                                                                             Exome Sequencing of 32 intrahepatic cholangiocarcinoma cases and 8 gall bladder carcinoma cases.
68                                                                                                                                                                         TCGA Kidney Chromophobe; raw data at the <A HREF="https://tcga-data.nci.nih.gov/tcga/tcgaCancerDetails.jsp?diseaseType=KICH&diseaseName=Kidney Chromophobe">NCI</A>.
69                                                                                                                                                                                                                                                   TCGA Kidney Chromophobe; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
70                                                                                                                                                                                                                                                  Comprehensive sequencing of 98 clear cell kidney cancer samples. Generated by BGI-Shenzhen.
71                                                                                                                   TCGA Kidney Renal Clear Cell Carcinoma, containing 499 samples; raw data at the <A HREF="https://tcga-data.nci.nih.gov/tcga/tcgaCancerDetails.jsp?diseaseType=KIRC&diseaseName=Kidney Renal Clear Cell Carcinoma">NCI</A>.
72                                                                                                                                                                                                                                    TCGA Kidney Renal Clear Cell Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
73                                                                                                                                                                                                                                TCGA Kidney Renal Papillary Cell Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
74                                                                                                                                                                                                                                                      Liver Hepatocellular Carcinoma from Asan Medical Center, Korea, containing 231 samples.
75                                                                                                                                                                                                                                                                   Whole-genome sequencing of 27 hepatocellular carcinoma samples from RIKEN.
76                                                                                                                                                                                                                                       TCGA Liver Hepatocellular Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
77                                                                                                                                                                                                                                                                    Mutation data from whole exome sequencing of 23 grade II glioma patients.
78                                                                                                                                                                                                                                                Comprehensive profiling of 183 lung adenocarcinoma samples. Generated by the Broad Institute.
79                                                                                                                                                                                                                                                             Whole-exome sequencing of non small cell lung cancers treated with pembrolizumab
80                                                                                                                                                TCGA Lung Adenocarcinoma, containing 230 samples; raw data at the <A HREF="https://tcga-data.nci.nih.gov/tcga/tcgaCancerDetails.jsp?diseaseType=LUAD&diseaseName=Lung Adenoarcinoma">NCI</A>.
81                                                                                                                                                                                                                                                  TCGA Lung Adenocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
82                                                                                                                                                                                                                                                            Targeted sequencing of 163 lung adenocarcinoma samples. Generated by WashU/Broad.
83                                                                                <a href="http://cancergenome.nih.gov/">The Cancer Genome Atlas (TCGA)</a> Lung Squamous Cell Carcinoma project. 178 cases.<br><i>Nature 2012.</i> <a href="https://tcga-data.nci.nih.gov/docs/publications/lusc_2012/">Raw data via the TCGA Data Portal</a>.
84                                                                                                                                                                                                                                         TCGA Lung Squamous Cell Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
85                                                                                                                                                                                                                      TCGA Lymphoid Neoplasm Diffuse Large B-cell Lymphoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
86                                                                                                                                                                                                                                                                      Targeted sequencing of 10,000 clinical cases using the MSK-IMPACT assay
87                                                                                                                                                                                                                                                                              Exome profiling of 17 malignant peripheral nerve sheath tumors.
88                                                                                                                                                                                                                          Mutation data from whole-exome sequencing of 22 malignant pleural mesotheliomas (PLMESO) and matched blood samples.
89                                                                                                                                                                                                                                                                                  Whole exome sequencing of 29 primary mantle cell lymphomas.
90                                                                                                                                                                                                                                                              Comprehensive profiling of 92 medulloblastoma samples from the Broad Institute.
91                                                                                                                                                                                                                                                                                              125 Medulloblastoma tumor / normal pairs. ICGC.
92                                                                                                                                                   Whole genome sequencing of 37 medulloblastoma samples from the Pediatric Cancer Genome Project (PCGP), a joint project by St. Jude Children's Research Hospital and Washington University.
93                                                                                                                                                                                                                                                    Mutation data from whole-genome sequencing (WGS) of 46 recurrent medulloblastoma samples.
94                                                                                                                                                                                                                                                             Somatic Mutation data from 25 Whole Genome Sequenced metastatic melanoma samples
95                                                                                                                                                                                                                                                                                           Whole-exome sequencing from TCGA LGG and GBM cases
96                                                                                                                                                                                                                                                         TCGA Mesothelioma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
97                                                                                                                                                                                                                                                  Comprehensive analysis of 150 metastatic prostate cancer samples by the SU2C/PCF Dream Team
98                                                                                                                                                                                                                                                                                            Exome sequencing of 205 multiple myeloma samples.
99                                                                                                                                                                                                                                             Mutation data from multi region exome sequencing of 10 clear cell renal cell carcinomas (ccRCCs)
100                                                      Whole-exome sequencing was performed on 216 tumor-normal (blood) pairs from metastatic breast cancer patients who underwent a biopsy in the context of the SAFIR01/SAFIR02 (Unicancer, France), SHIVA (Institut Curie, France) or MOSCATO (Gustave Roussy, France) prospective trials.
101                                                                                                                                                                                                                                                           Whole exome sequencing of 29 myelodysplasia samples from the University of Tokyo.
102                                                                                                                                                                                                                        NCI-60 cell line project; raw data at <A HREF="http://discover.nci.nih.gov/cellminer/loadDownload.do">CellMiner</A>.
103                                                                                                                                                                                           Whole genome sequencing of 56 NPC tumor / normal pairs. Generated by the Cancer Science Institute of Singapore, National University of Singapore.
104                                                                                                                                                                                                                                            Whole genome sequencing of 87 neuroblastoma samples from the Academic Medical Center, Amsterdam.
105                                                                                                                                                                                                                                                                      Mutation data from whole-genome sequencing of 56 neuroblastoma samples
106                                                                                                                                                                 Whole exome and RNA Seq data of castration resistant adenocarcinoma and castration resistant neuroendocrine prostate cancer (somatic mutations and copy number aberrations)
107                                                                                                                                                                                                                                                        Comprehensive profiling of 40 oral squamous cell carcinoma samples from MD Anderson.
108                                                                                                           <a href="http://cancergenome.nih.gov/">The Cancer Genome Atlas (TCGA)</a> Serous Ovarian Cancer project. 489 cases.<br> <a href="https://tcga-data.nci.nih.gov/docs/publications/ov_2011/">Raw data via the TCGA Data Portal</a>.
109                                                                                                                                                                                                                                   TCGA Ovarian Serous Cystadenocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
110                                                                                                                                                                                                                                                            Somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas.
111                                                                                                                                                                                                                                                                 Comprehensive profiling of 99 pancreatic cancer samples. Generated by ICGC.
112                                                                                                                          342 primary tumours and 41 patient-derived cell lines underwent whole genome sequencing (WGS) when tumour cellularity was >40% (n=179), or deep-exome sequencing (n=204) for samples with a cellularity of 12-40%.
113                                                                                                                                                                                                                                           TCGA Pancreatic Adenocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
114                                                                                                                                                                                                                                            Whole exome sequencing of 109 micro-dissected pancreatic cancer cases and normal control tissue.
115                                                                                                                                                                                                Whole exome sequencing of 10 pancreatic neuroendocrine tumor patients. <A HREF="https://www.sciencemag.org/content/331/6021/1199/suppl/DC1">
116                                                                                                                                      TCGA Papillary Thyroid Carcinoma, containing 230 samples; raw data at the <A HREF="https://tcga-data.nci.nih.gov/tcga/tcgaCancerDetails.jsp?diseaseType=THCA&diseaseName=Thyroid%20carcinoma">NCI</A>.
117                                                                                                                                                                                                                                                              Whole exome sequencing of 96 pediatric Ewing Sarcoma tumors and 11 cell lines.
118                                                                                                                                                                                                                                  TCGA Pheochromocytoma and Paraganglioma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
119                                                                                                                                                                                                                          Next generation sequencing (MSK-IMPACT) of 84 poorly-differentiated (PDTC) and 33 anaplastic thyroid cancers (ATC)
120                                                                                                                                                                                                              Mutation data from whole exome sequencing (WXS) of 10 immunocompetent primary central nervous system lymphoma (PCNSL) samples.
121                                                                                                                                                                                             Comprehensive profiling of 57 prostate cancer samples. Generated by Levi Garraway's lab at the Broad Institute and Mark Rubin's lab at Cornell.
122                                                                                                                                                                                            Comprehensive profiling of 112 prostate cancer samples. Generated by Levi Garraway's lab at the Broad Institute and Mark Rubin's lab at Cornell.
123                                                                                                                                                                                                          Comprehensive profiling of prostate cancer samples. Generated by Peter Nelson's lab at the Fred Hutchinson Cancer Research Center.
124 MSKCC Prostate Oncogenome Project. 181 primary, 37 metastatic prostate cancer samples, 12 prostate cancer cell lines and xenografts.<br><a href="http://cbio.mskcc.org/cancergenomics/prostate/data/">Normalized flat data files</a>. <a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21032">Raw data via GEO (GSE21032)</a>.
125                                                                                                                                                                          Integrated profiling of 333 primary prostate adenocarcinoma samples; raw data at the <A HREF="https://tcga-data.nci.nih.gov/docs/publications/prad_2015/">NCI</A>.
126                                                                                                                                                                                                                                             TCGA Prostate Adenocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
127                                                                                                                                                              Copy-number profiling of 103 primary prostate cancer samples from MSKCC. <a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54691">Raw data via GEO (GSE54691)</a>.
128                                                                                                                                                                                                                                                                           Exome profiling of prostate cancer samples and matched organoids.
129                                                                                                                    Comprehensive profiling of 61 prostate cancer samples, including 50 metastatic CRPCs and 11 high-grade localized prostate cancers. Generated by Arul Chinnaiyan's and Scott Tomlins' labs at the University of Michigan.
130                                                                                                                                                                                                                                                 Targeted sequencing of 151 patients with advanced, treatment resistant head and neck tumors
131                                                                                                                                                                                                                                                                    Exome sequencing of 139 Renal Non-Clear Cell Carcinoma (NCCRCC) samples.
132                                                                                                                                                                                                                                                                           Mutation data from WGS and/or WXS of 43 rhabdomyosarcoma samples.
133           The Sarcoma Genome Project, <a href="http://www.mskcc.org/">MSKCC</a> and <a href="http://www.broadinstitute.org/">The Broad Institute</a>. 207 high-grade adult soft tissue sarcomas across seven subtypes of disease.<br> <a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21124">Raw data via GEO (GSE21124)</a>.
134                                                                                                                                                                                                                                                             TCGA Sarcoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
135                                                                                                                                                                                                                                                          Comprehensive profiling of 121 melanoma samples. Generated by the Broad Institute.
136                                                                                                                                                                                                                                             TCGA Skin Cutaneous Melanoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
137                                                                                                                                                                                                                                                                                 Exome sequencing of 91 melanoma samples. Generated by Yale.
138                                                                                                                                                                                                                                                                                                     Targeted sequencing of 12 SCCO samples.
139                                                                                                                                                                                                                         Comprehensive profiling of 29 small cell lung cancer samples. Generated by the Clinical Lung Cancer Genome Project.
140                                                                                                                                                                                                      Comprehensive profiling of 36 primary human SCLC tumors and 17 matched SCLC and lymphoblastoid cell lines. Generated by Johns Hopkins.
141                                                                                                                                                                                                                                                                                    Comprehensive WGS profiling of 110 human SCLC specimens.
142                                                                                                                                                                                                                                              Whole genome sequencing of 100 tumor-normal pairs from the University of Hong Kong and Pfizer.
143                                                                                                                                                                                          TCGA Stomach Adenocarcinoma, containing 295 samples; raw data at the <A HREF="https://tcga-data.nci.nih.gov/docs/publications/stad_2014/">NCI</A>.
144                                                                                                                                                                                                                                              TCGA Stomach Adenocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
145                                                                                                                                                                                                                                      Whole exome sequencing of 30 diffuse-type gastric adenocarcinoma samples from the University of Tokyo.
146                                                                                                                                                                                                                                                                                              Exome sequencing of 22 gastric cancer samples.
147                                                                                                                                                                                                                                                                                                    TCGA data for Esophagus-Stomach Cancers.
148                                                                                                                                                                                                                                         TCGA Testicular Germ Cell Cancer; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
149                                                                                                                                                                                                                                                                                      Whole exome sequencing of 28 thymic epithelial tumors.
150                                                                                                                                                                                                                                                             TCGA Thymoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
151                                                                                                                                                                                                                                                   TCGA Thyroid Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
152                                                                                                                                                                                                                                                                                     Molecular Analysis of Unclassified Renal Cell Carcinoma
153                                                                                                                                           Whole exome sequencing (WXS) of 22 uterine carcinosarcoma/uterine malignant mixed Mullerian (UCS) tumors. <A HREF="http://www.nature.com/ncomms/2014/140919/ncomms6006/extref/ncomms6006-s1.pdf">
154                                                                                                                                                                                                                                              TCGA Uterine Carcinosarcoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
155                                                                                                                                                                            TCGA Uterine Corpus Endometrial Carcinoma, containing 373 samples; raw data at the <A HREF="https://tcga-data.nci.nih.gov/docs/publications/ucec_2013/">NCI</A>.
156                                                                                                                                                                                                                                TCGA Uterine Corpus Endometrial Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
157                                                                                                                                                                                                                                                      TCGA Uveal Melanoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
158                                                                                                                                                                                                                         Whole-genome sequencing of 102 primary PanNETs and the defined genomic events that characterize their pathogenesis.
159                                                                                                                                                        Whole-genome sequencing of 96 pilocytic astrocytomasatic alterations in pilocytic astrocytoma conducted by the International Cancer Genome Consortium (ICGC) PedBrain Tumor Project.
> 
> # Get available case lists (collection of samples) for a given cancer study
> mycancerstudy = getCancerStudies(mycgds)[2,1]
Warning in file(file, "rt") :
  InternetOpenUrl failed: 'Das Zeitlimit für den Vorgang wurde erreicht.'
Error in file(file, "rt") : cannot open the connection
Calls: getCancerStudies ... processURL -> processURL.CGDS -> read.table -> file
Execution halted