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  133. <h1 id="seo-header">通过conda安装纯净环境的CellChat</h1>
  134. <div class="markdown-body">
  135. <ul>
  136. <li><a target="_blank" rel="noopener" href="https://anaconda.org/conda-forge/r-base">https://anaconda.org/conda-forge/r-base</a></li>
  137. <li>conda create -n cellchat -c conda-forge r-base&#x3D;4.1.2 -y</li>
  138. <li>conda activate cellchat</li>
  139. <li>conda install -c conda-forge r-seurat&#x3D;4.1.0 -y</li>
  140. <li>conda install -c conda-forge r-irkernel&#x3D;1.3 -y</li>
  141. <li>conda install -c conda-forge r-biocmanager&#x3D;1.30.16 -y</li>
  142. <li>conda install -c conda-forge r-devtools&#x3D;2.4.3 -y</li>
  143. <li>conda install -c conda-forge r-circlize&#x3D;0.4.14 -y</li>
  144. <li>conda install -c conda-forge umap-learn&#x3D;0.5.3 -y</li>
  145. <li>conda install -c bioconda bioconductor-biobase&#x3D;2.54.0 -y</li>
  146. <li>wget <a target="_blank" rel="noopener" href="https://github.com/sqjin/CellChat/archive/refs/heads/master.zip">https://github.com/sqjin/CellChat/archive/refs/heads/master.zip</a> -O CellChat-master.zip</li>
  147. <li><strong>移除CellChat-master.zip里src目录下的*.so和*.o文件</strong></li>
  148. <li>unzip CellChat-master.zip</li>
  149. <li>rm CellChat-master&#x2F;src&#x2F;*.so</li>
  150. <li>rm CellChat-master&#x2F;src&#x2F;*.o</li>
  151. <li>wget <a target="_blank" rel="noopener" href="https://github.com/jokergoo/ComplexHeatmap/archive/refs/heads/master.zip">https://github.com/jokergoo/ComplexHeatmap/archive/refs/heads/master.zip</a> -O ComplexHeatmap-master.zip</li>
  152. <li>conda install -c conda-forge r-svglite&#x3D;2.1.0 -y</li>
  153. <li>install.packages(‘NMF’)</li>
  154. <li>devtools::install_local(‘ComplexHeatmap-master.zip’)</li>
  155. <li>devtools::install_local(‘CellChat-master’)</li>
  156. <li>IRkernel::installspec(name&#x3D;’cellchat’, displayname&#x3D;’r-cellchat’)</li>
  157. </ul>
  158. <figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br></pre></td><td class="code"><pre><code class="hljs r">Sys.setenv<span class="hljs-punctuation">(</span>RETICULATE_PYTHON <span class="hljs-operator">=</span> <span class="hljs-string">&quot;/opt/conda/envs/cellchat/bin/python3.7&quot;</span><span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;reticulate&#x27;</span><span class="hljs-punctuation">)</span><br>use_condaenv<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;cellchat&quot;</span><span class="hljs-punctuation">)</span><br>py_config<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
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  170. <a href="/categories/%E7%BB%86%E8%83%9E%E9%80%9A%E8%AE%AF/" class="category-chain-item">细胞通讯</a>
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  315. <script src="https://lib.baomitu.com/typed.js/2.0.12/typed.min.js" ></script>
  316. <script>
  317. (function (window, document) {
  318. var typing = Fluid.plugins.typing;
  319. var subtitle = document.getElementById('subtitle');
  320. if (!subtitle || !typing) {
  321. return;
  322. }
  323. var text = subtitle.getAttribute('data-typed-text');
  324. typing(text);
  325. })(window, document);
  326. </script>
  327. <script src="/js/img-lazyload.js" ></script>
  328. <script>
  329. Fluid.utils.createScript('https://jscdn.limour.top/npm/tocbot@4.20.1/dist/tocbot.min.js', function() {
  330. var toc = jQuery('#toc');
  331. if (toc.length === 0 || !window.tocbot) { return; }
  332. var boardCtn = jQuery('#board-ctn');
  333. var boardTop = boardCtn.offset().top;
  334. window.tocbot.init(Object.assign({
  335. tocSelector : '#toc-body',
  336. contentSelector : '.markdown-body',
  337. linkClass : 'tocbot-link',
  338. activeLinkClass : 'tocbot-active-link',
  339. listClass : 'tocbot-list',
  340. isCollapsedClass: 'tocbot-is-collapsed',
  341. collapsibleClass: 'tocbot-is-collapsible',
  342. scrollSmooth : true,
  343. includeTitleTags: true,
  344. headingsOffset : -boardTop,
  345. }, CONFIG.toc));
  346. if (toc.find('.toc-list-item').length > 0) {
  347. toc.css('visibility', 'visible');
  348. }
  349. Fluid.events.registerRefreshCallback(function() {
  350. if ('tocbot' in window) {
  351. tocbot.refresh();
  352. var toc = jQuery('#toc');
  353. if (toc.length === 0 || !tocbot) {
  354. return;
  355. }
  356. if (toc.find('.toc-list-item').length > 0) {
  357. toc.css('visibility', 'visible');
  358. }
  359. }
  360. });
  361. });
  362. </script>
  363. <script src=https://lib.baomitu.com/clipboard.js/2.0.11/clipboard.min.js></script>
  364. <script>Fluid.plugins.codeWidget();</script>
  365. <script>
  366. Fluid.utils.createScript('https://jscdn.limour.top/npm/anchor-js@4.3.1/anchor.min.js', function() {
  367. window.anchors.options = {
  368. placement: CONFIG.anchorjs.placement,
  369. visible : CONFIG.anchorjs.visible
  370. };
  371. if (CONFIG.anchorjs.icon) {
  372. window.anchors.options.icon = CONFIG.anchorjs.icon;
  373. }
  374. var el = (CONFIG.anchorjs.element || 'h1,h2,h3,h4,h5,h6').split(',');
  375. var res = [];
  376. for (var item of el) {
  377. res.push('.markdown-body > ' + item.trim());
  378. }
  379. if (CONFIG.anchorjs.placement === 'left') {
  380. window.anchors.options.class = 'anchorjs-link-left';
  381. }
  382. window.anchors.add(res.join(', '));
  383. Fluid.events.registerRefreshCallback(function() {
  384. if ('anchors' in window) {
  385. anchors.removeAll();
  386. var el = (CONFIG.anchorjs.element || 'h1,h2,h3,h4,h5,h6').split(',');
  387. var res = [];
  388. for (var item of el) {
  389. res.push('.markdown-body > ' + item.trim());
  390. }
  391. if (CONFIG.anchorjs.placement === 'left') {
  392. anchors.options.class = 'anchorjs-link-left';
  393. }
  394. anchors.add(res.join(', '));
  395. }
  396. });
  397. });
  398. </script>
  399. <script>
  400. Fluid.utils.createScript('https://lib.baomitu.com/fancybox/3.5.7/jquery.fancybox.min.js', function() {
  401. Fluid.plugins.fancyBox();
  402. });
  403. </script>
  404. <script>Fluid.plugins.imageCaption();</script>
  405. <script src="/js/local-search.js" ></script>
  406. <!-- 主题的启动项,将它保持在最底部 -->
  407. <!-- the boot of the theme, keep it at the bottom -->
  408. <script src="/js/boot.js" ></script>
  409. <noscript>
  410. <div class="noscript-warning">Blog works best with JavaScript enabled</div>
  411. </noscript>
  412. <!-- hexo injector body_end start -->
  413. <script defer src="/theme-inject/timeliness.js"></script>
  414. <!-- hexo injector body_end end --></body>
  415. </html>