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Created May 6, 2016 20:56
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Getting a list of all TCGA studies and their abbreviations via pytcga
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studies.ipynb
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"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>Study Abbreviation</th>\n",
" <th>Study Name</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>ACC</td>\n",
" <td>Adrenocortical carcinoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>BLCA</td>\n",
" <td>Bladder Urothelial Carcinoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>BRCA</td>\n",
" <td>Breast invasive carcinoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>CESC</td>\n",
" <td>Cervical squamous cell carcinoma and endocervi...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>CHOL</td>\n",
" <td>Cholangiocarcinoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>CNTL</td>\n",
" <td>Controls</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>COAD</td>\n",
" <td>Colon adenocarcinoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>DLBC</td>\n",
" <td>Lymphoid Neoplasm Diffuse Large B-cell Lymphoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>ESCA</td>\n",
" <td>Esophageal carcinoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
" <td>GBM</td>\n",
" <td>Glioblastoma multiforme</td>\n",
" </tr>\n",
" <tr>\n",
" <th>10</th>\n",
" <td>HNSC</td>\n",
" <td>Head and Neck squamous cell carcinoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>11</th>\n",
" <td>KICH</td>\n",
" <td>Kidney Chromophobe</td>\n",
" </tr>\n",
" <tr>\n",
" <th>12</th>\n",
" <td>KIRC</td>\n",
" <td>Kidney renal clear cell carcinoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>13</th>\n",
" <td>KIRP</td>\n",
" <td>Kidney renal papillary cell carcinoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>14</th>\n",
" <td>LAML</td>\n",
" <td>Acute Myeloid Leukemia</td>\n",
" </tr>\n",
" <tr>\n",
" <th>15</th>\n",
" <td>LGG</td>\n",
" <td>Brain Lower Grade Glioma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>16</th>\n",
" <td>LIHC</td>\n",
" <td>Liver hepatocellular carcinoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>17</th>\n",
" <td>LUAD</td>\n",
" <td>Lung adenocarcinoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>18</th>\n",
" <td>LUSC</td>\n",
" <td>Lung squamous cell carcinoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>19</th>\n",
" <td>MESO</td>\n",
" <td>Mesothelioma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>20</th>\n",
" <td>OV</td>\n",
" <td>Ovarian serous cystadenocarcinoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>21</th>\n",
" <td>PAAD</td>\n",
" <td>Pancreatic adenocarcinoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>22</th>\n",
" <td>PCPG</td>\n",
" <td>Pheochromocytoma and Paraganglioma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23</th>\n",
" <td>PRAD</td>\n",
" <td>Prostate adenocarcinoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>24</th>\n",
" <td>READ</td>\n",
" <td>Rectum adenocarcinoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>25</th>\n",
" <td>SARC</td>\n",
" <td>Sarcoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>26</th>\n",
" <td>SKCM</td>\n",
" <td>Skin Cutaneous Melanoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>27</th>\n",
" <td>STAD</td>\n",
" <td>Stomach adenocarcinoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>28</th>\n",
" <td>TGCT</td>\n",
" <td>Testicular Germ Cell Tumors</td>\n",
" </tr>\n",
" <tr>\n",
" <th>29</th>\n",
" <td>THCA</td>\n",
" <td>Thyroid carcinoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>30</th>\n",
" <td>THYM</td>\n",
" <td>Thymoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>31</th>\n",
" <td>UCEC</td>\n",
" <td>Uterine Corpus Endometrial Carcinoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>32</th>\n",
" <td>UCS</td>\n",
" <td>Uterine Carcinosarcoma</td>\n",
" </tr>\n",
" <tr>\n",
" <th>33</th>\n",
" <td>UVM</td>\n",
" <td>Uveal Melanoma</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" Study Abbreviation Study Name\n",
"0 ACC Adrenocortical carcinoma\n",
"1 BLCA Bladder Urothelial Carcinoma\n",
"2 BRCA Breast invasive carcinoma\n",
"3 CESC Cervical squamous cell carcinoma and endocervi...\n",
"4 CHOL Cholangiocarcinoma\n",
"5 CNTL Controls\n",
"6 COAD Colon adenocarcinoma\n",
"7 DLBC Lymphoid Neoplasm Diffuse Large B-cell Lymphoma\n",
"8 ESCA Esophageal carcinoma \n",
"9 GBM Glioblastoma multiforme\n",
"10 HNSC Head and Neck squamous cell carcinoma\n",
"11 KICH Kidney Chromophobe\n",
"12 KIRC Kidney renal clear cell carcinoma\n",
"13 KIRP Kidney renal papillary cell carcinoma\n",
"14 LAML Acute Myeloid Leukemia\n",
"15 LGG Brain Lower Grade Glioma\n",
"16 LIHC Liver hepatocellular carcinoma\n",
"17 LUAD Lung adenocarcinoma\n",
"18 LUSC Lung squamous cell carcinoma\n",
"19 MESO Mesothelioma\n",
"20 OV Ovarian serous cystadenocarcinoma\n",
"21 PAAD Pancreatic adenocarcinoma\n",
"22 PCPG Pheochromocytoma and Paraganglioma\n",
"23 PRAD Prostate adenocarcinoma\n",
"24 READ Rectum adenocarcinoma\n",
"25 SARC Sarcoma\n",
"26 SKCM Skin Cutaneous Melanoma\n",
"27 STAD Stomach adenocarcinoma\n",
"28 TGCT Testicular Germ Cell Tumors\n",
"29 THCA Thyroid carcinoma\n",
"30 THYM Thymoma\n",
"31 UCEC Uterine Corpus Endometrial Carcinoma\n",
"32 UCS Uterine Carcinosarcoma\n",
"33 UVM Uveal Melanoma"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"import pytcga\n",
"pytcga.load_studies()"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 2",
"language": "python",
"name": "python2"
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"language_info": {
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"name": "ipython",
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"file_extension": ".py",
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"nbconvert_exporter": "python",
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