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  133. <h1 id="seo-header">TCGA突变数据使用记录(一)</h1>
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  135. <h2 id="数据下载,从cBioPortal"><a href="#数据下载,从cBioPortal" class="headerlink" title="数据下载,从cBioPortal"></a>数据下载,从cBioPortal</h2><ul>
  136. <li>从<a target="_blank" rel="noopener" href="https://www.cbioportal.org/">cBioPortal</a>找到相应的数据,并从<a target="_blank" rel="noopener" href="https://github.com/cBioPortal/datahub/tree/master/public">github</a>下载</li>
  137. <li>~&#x2F;dev&#x2F;xray&#x2F;xray -c ~&#x2F;etc&#x2F;xui2.json &amp;</li>
  138. <li>wget -e “https_proxy&#x3D;<a target="_blank" rel="noopener" href="http://127.0.0.1:20809/">http://127.0.0.1:20809</a>“ <a target="_blank" rel="noopener" href="https://github.com/cBioPortal/datahub/raw/master/public/prad/_tcga/data/_mutations.txt">https://github.com/cBioPortal/datahub/raw/master/public/prad\_tcga/data\_mutations.txt</a></li>
  139. <li>tmp &lt;- read.table(‘data_mutations.txt’, header &#x3D; T, sep &#x3D; ‘\t’, allowEscapes &#x3D; T, quote &#x3D; ‘’)</li>
  140. </ul>
  141. <h2 id="数据下载,从TCGA"><a href="#数据下载,从TCGA" class="headerlink" title="数据下载,从TCGA"></a>数据下载,从TCGA</h2><ul>
  142. <li>访问<a target="_blank" rel="noopener" href="https://portal.gdc.cancer.gov/repository">TCGA</a>,在文件类型中过滤maf,访问权限中过滤open,case中过滤感兴趣的组织</li>
  143. <li>加入到cart,然后可以直接下载tar.gz,也可以下载<strong>manifest</strong>,然后<a target="_blank" rel="noopener" href="http://www.bio-info-trainee.com/2513.html">使用</a><a target="_blank" rel="noopener" href="https://gdc.cancer.gov/access-data/gdc-data-transfer-tool">官方工具</a>下载</li>
  144. <li>后续可以使用Maftools进行分析</li>
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  197. <article class="post-prev col-6">
  198. <a href="/2008.html" title="TCGAbiolinks下载maf数据">
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  200. <span class="hidden-mobile">TCGAbiolinks下载maf数据</span>
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  330. if (toc.find('.toc-list-item').length > 0) {
  331. toc.css('visibility', 'visible');
  332. }
  333. Fluid.events.registerRefreshCallback(function() {
  334. if ('tocbot' in window) {
  335. tocbot.refresh();
  336. var toc = jQuery('#toc');
  337. if (toc.length === 0 || !tocbot) {
  338. return;
  339. }
  340. if (toc.find('.toc-list-item').length > 0) {
  341. toc.css('visibility', 'visible');
  342. }
  343. }
  344. });
  345. });
  346. </script>
  347. <script src=https://lib.baomitu.com/clipboard.js/2.0.11/clipboard.min.js></script>
  348. <script>Fluid.plugins.codeWidget();</script>
  349. <script>
  350. Fluid.utils.createScript('https://jscdn.limour.top/npm/anchor-js@4.3.1/anchor.min.js', function() {
  351. window.anchors.options = {
  352. placement: CONFIG.anchorjs.placement,
  353. visible : CONFIG.anchorjs.visible
  354. };
  355. if (CONFIG.anchorjs.icon) {
  356. window.anchors.options.icon = CONFIG.anchorjs.icon;
  357. }
  358. var el = (CONFIG.anchorjs.element || 'h1,h2,h3,h4,h5,h6').split(',');
  359. var res = [];
  360. for (var item of el) {
  361. res.push('.markdown-body > ' + item.trim());
  362. }
  363. if (CONFIG.anchorjs.placement === 'left') {
  364. window.anchors.options.class = 'anchorjs-link-left';
  365. }
  366. window.anchors.add(res.join(', '));
  367. Fluid.events.registerRefreshCallback(function() {
  368. if ('anchors' in window) {
  369. anchors.removeAll();
  370. var el = (CONFIG.anchorjs.element || 'h1,h2,h3,h4,h5,h6').split(',');
  371. var res = [];
  372. for (var item of el) {
  373. res.push('.markdown-body > ' + item.trim());
  374. }
  375. if (CONFIG.anchorjs.placement === 'left') {
  376. anchors.options.class = 'anchorjs-link-left';
  377. }
  378. anchors.add(res.join(', '));
  379. }
  380. });
  381. });
  382. </script>
  383. <script>
  384. Fluid.utils.createScript('https://lib.baomitu.com/fancybox/3.5.7/jquery.fancybox.min.js', function() {
  385. Fluid.plugins.fancyBox();
  386. });
  387. </script>
  388. <script>Fluid.plugins.imageCaption();</script>
  389. <script src="/js/local-search.js" ></script>
  390. <!-- 主题的启动项,将它保持在最底部 -->
  391. <!-- the boot of the theme, keep it at the bottom -->
  392. <script src="/js/boot.js" ></script>
  393. <noscript>
  394. <div class="noscript-warning">Blog works best with JavaScript enabled</div>
  395. </noscript>
  396. <!-- hexo injector body_end start -->
  397. <script defer src="/theme-inject/timeliness.js"></script>
  398. <!-- hexo injector body_end end --></body>
  399. </html>