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            <h1 id="seo-header">通过conda安装纯净环境的imputation</h1>
            
            
              <div class="markdown-body">
                
                <p><a target="_blank" rel="noopener" href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02132-x">https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02132-x</a></p>
<h2 id="SAVER-X"><a href="#SAVER-X" class="headerlink" title="SAVER-X"></a>SAVER-X</h2><p><a target="_blank" rel="noopener" href="https://github.com/jingshuw/SAVERX">https://github.com/jingshuw/</a><a target="_blank" rel="noopener" href="https://github.com/jingshuw/SAVERX">SAVERX</a></p>
<ul>
<li><p>conda create -n imputation -c conda-forge r-base&#x3D;4.1.3 -y</p>
</li>
<li><p>conda activate imputation</p>
</li>
<li><p>conda install -c conda-forge r-seurat&#x3D;4.1.0 -y</p>
</li>
<li><p>conda install -c conda-forge r-tidyverse&#x3D;1.3.1 -y</p>
</li>
<li><p>conda install -c conda-forge r-biocmanager&#x3D;1.30.16 -y</p>
</li>
<li><p>conda install -c conda-forge r-devtools&#x3D;2.4.3 -y</p>
</li>
<li><p>conda install -c conda-forge r-reticulate&#x3D;1.24 -y</p>
</li>
<li><p>conda install -c conda-forge r-irkernel&#x3D;1.3 -y</p>
</li>
<li><p>wget <a target="_blank" rel="noopener" href="https://github.com/jingshuw/SAVERX/archive/refs/heads/master.zip">https://github.com/jingshuw/SAVERX/archive/refs/heads/master.zip</a> -O SAVERX-master.zip</p>
</li>
<li><p>devtools::install_local(“SAVERX-master.zip”)</p>
</li>
<li><p>IRkernel::installspec(name&#x3D;’imputation’, displayname&#x3D;’r-imputation’)</p>
</li>
<li><p># IO错误 请修改xui2.json内的DNS服务器ip</p>
</li>
<li><p>~&#x2F;dev&#x2F;xray&#x2F;xray -c ~&#x2F;etc&#x2F;xui2.json &amp;</p>
</li>
<li><p>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://www.dropbox.com/sh/4u22cfuswcfcwvu/AAC4hl-f7P5lD8EZU1CFVt6-a/human/_Immune.hdf5?dl=0">https://www.dropbox.com/sh/4u22cfuswcfcwvu/AAC4hl-f7P5lD8EZU1CFVt6-a/human\_Immune.hdf5?dl=0</a> -O human_Immune.hdf5</p>
</li>
<li><p>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://www.dropbox.com/sh/4u22cfuswcfcwvu/AABv0YxcNAChwEPS-D9hnDM6a/human/_Tcells.hdf5?dl=0">https://www.dropbox.com/sh/4u22cfuswcfcwvu/AABv0YxcNAChwEPS-D9hnDM6a/human\_Tcells.hdf5?dl=0</a> -O human_Tcells.hdf5</p>
</li>
<li><p>fg</p>
</li>
<li><p><strong>垃圾程序让人高血压！！！</strong></p>
</li>
<li><p>conda deactivate</p>
</li>
<li><p>conda create -n imputation_saver_x -c conda-forge python&#x3D;3.7 -y</p>
</li>
<li><p>conda activate imputation_saver_x</p>
</li>
<li><p>pip install scanpy&#x3D;&#x3D;1.4.4</p>
</li>
<li><p>pip install tensorflow&#x3D;&#x3D;2.1.0</p>
</li>
<li><p>pip install Keras&#x3D;&#x3D;2.3.1</p>
</li>
<li><p><a target="_blank" rel="noopener" href="https://github.com/tensorflow/tensorflow/issues/38589">https://github.com/tensorflow/tensorflow/issues/38589</a></p>
</li>
<li><p>nano -K &#x2F;opt&#x2F;conda&#x2F;envs&#x2F;imputation_saver_x&#x2F;lib&#x2F;python3.7&#x2F;site-packages&#x2F;keras&#x2F;backend&#x2F;tensorflow_backend.py</p>
</li>
<li><p>按说明重定义 is_tensor 函数</p>
</li>
<li><p>pip install sctransfer</p>
</li>
<li><p>修改 &#x2F;opt&#x2F;conda&#x2F;envs&#x2F;imputation_saver_x&#x2F;lib&#x2F;python3.7&#x2F;site-packages&#x2F;keras&#x2F;engine&#x2F;saving.py</p>
</li>
<li><p>删除全部的 .decode(‘utf8’)和.encode(‘utf8’)</p>
</li>
<li><p>conda deactivate</p>
</li>
<li><p>conda create -n imputation_saver_x -c conda-forge python&#x3D;3.7 -y</p>
</li>
<li><p>conda activate imputation_saver_x</p>
</li>
<li><p>pip install scanpy&#x3D;&#x3D;1.4.4</p>
</li>
<li><p>pip install tensorflow&#x3D;&#x3D;1.15.0</p>
</li>
<li><p>pip install Keras&#x3D;&#x3D;2.3.1</p>
</li>
<li><p>pip install sctransfer</p>
</li>
</ul>
<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><span class="line">5</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/imputation_saver_x/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;imputation_saver_x&quot;</span><span class="hljs-punctuation">)</span><br>py_config<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>SAVERX<span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="MAGIC"><a href="#MAGIC" class="headerlink" title="MAGIC"></a>MAGIC</h2><p><a target="_blank" rel="noopener" href="http://htmlpreview.github.io/?https://github.com/KrishnaswamyLab/MAGIC/blob/master/Rmagic/inst/examples/bonemarrow_tutorial.html">http://htmlpreview.github.io/?https://github.com/KrishnaswamyLab/MAGIC/blob/master/Rmagic/inst/examples/bonemarrow_tutorial.html</a></p>
<ul>
<li>conda deactivate</li>
<li>conda activate imputation</li>
<li>conda install -c conda-forge r-viridis&#x3D;0.6.2 -y</li>
<li>conda install -c conda-forge r-ggplot2&#x3D;3.3.5 -y</li>
<li>conda install -c conda-forge r-readr&#x3D;2.1.2 -y</li>
<li>conda install -c conda-forge r-phater&#x3D;1.0.7 -y</li>
<li>conda deactivate</li>
<li>conda create -n imputation_magic -c conda-forge numpy&#x3D;1.22.3 -y</li>
<li>conda activate imputation_magic</li>
<li>pip install phate</li>
<li>pip install magic-impute</li>
</ul>
<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><span class="line">5</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/imputation_magic/bin/python3.8&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;imputation_magic&quot;</span><span class="hljs-punctuation">)</span><br>py_config<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>Rmagic<span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="harmony"><a href="#harmony" class="headerlink" title="harmony"></a>harmony</h2><ul>
<li>conda install -c bioconda r-harmony -y</li>
</ul>
<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><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br></pre></td><td class="code"><pre><code class="hljs r">require<span class="hljs-punctuation">(</span>tidyverse<span class="hljs-punctuation">)</span><br>f_ScaleData_RunPCA <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    scRNA <span class="hljs-operator">&lt;-</span> FindVariableFeatures<span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">,</span> selection.method <span class="hljs-operator">=</span> <span class="hljs-string">&quot;vst&quot;</span><span class="hljs-punctuation">,</span> nfeatures <span class="hljs-operator">=</span> <span class="hljs-number">2000</span><span class="hljs-punctuation">)</span><br>    lc_all.genes <span class="hljs-operator">&lt;-</span> rownames<span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">)</span><br>    scRNA <span class="hljs-operator">&lt;-</span> ScaleData<span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">,</span> features <span class="hljs-operator">=</span> lc_all.genes<span class="hljs-punctuation">)</span><br> <br>    scRNA <span class="hljs-operator">&lt;-</span> RunPCA<span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">,</span> features <span class="hljs-operator">=</span> VariableFeatures<span class="hljs-punctuation">(</span>object <span class="hljs-operator">=</span> scRNA<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    print<span class="hljs-punctuation">(</span>ElbowPlot<span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">,</span> ndims <span class="hljs-operator">=</span> <span class="hljs-number">40</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    scRNA<br><span class="hljs-punctuation">&#125;</span><br><br>require<span class="hljs-punctuation">(</span>harmony<span class="hljs-punctuation">)</span><br>f_RunHarmony <span class="hljs-operator">&lt;-</span>  <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">,</span> dims<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">30</span><span class="hljs-punctuation">,</span> batchN<span class="hljs-operator">=</span><span class="hljs-string">&quot;batch&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    scRNA <span class="hljs-operator">=</span> scRNA <span class="hljs-operator">%&gt;%</span> RunHarmony<span class="hljs-punctuation">(</span>batchN<span class="hljs-punctuation">,</span> plot_convergence <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span><span class="hljs-punctuation">,</span> max.iter.harmony <span class="hljs-operator">=</span> <span class="hljs-number">30</span><span class="hljs-punctuation">)</span><br>    scRNA <span class="hljs-operator">&lt;-</span> scRNA <span class="hljs-operator">%&gt;%</span> RunUMAP<span class="hljs-punctuation">(</span>reduction <span class="hljs-operator">=</span> <span class="hljs-string">&quot;harmony&quot;</span><span class="hljs-punctuation">,</span> dims <span class="hljs-operator">=</span> dims<span class="hljs-punctuation">)</span><br>    scRNA<br><span class="hljs-punctuation">&#125;</span><br><br>f_FindNeighbors <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">,</span> resolution <span class="hljs-operator">=</span> <span class="hljs-number">0.5</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    scRNA <span class="hljs-operator">&lt;-</span> scRNA <span class="hljs-operator">%&gt;%</span> FindNeighbors<span class="hljs-punctuation">(</span>reduction <span class="hljs-operator">=</span> <span class="hljs-string">&quot;harmony&quot;</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">%&gt;%</span>  FindClusters<span class="hljs-punctuation">(</span>resolution <span class="hljs-operator">=</span> resolution<span class="hljs-punctuation">)</span><br>    scRNA<span class="hljs-punctuation">[[</span>paste0<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;h_resolution_&#x27;</span><span class="hljs-punctuation">,</span> resolution<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> Idents<span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">)</span><br>    scRNA<br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>
                
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