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            <h1 id="seo-header">通过conda安装纯净环境的SCENIC</h1>
            
            
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                <ul>
<li><a target="_blank" rel="noopener" href="https://scenic.aertslab.org/tutorials/">https://scenic.aertslab.org/tutorials/</a></li>
<li><a target="_blank" rel="noopener" href="https://anaconda.org/conda-forge/r-base">https://anaconda.org/conda-forge/r-base</a></li>
<li>conda create -n scenic -c conda-forge r-base&#x3D;4.1.2 -y</li>
<li>conda activate scenic</li>
<li>conda install -c conda-forge r-seurat&#x3D;4.1.0 -y</li>
<li>conda install -c conda-forge r-irkernel&#x3D;1.3 -y</li>
<li>conda install -c conda-forge r-biocmanager&#x3D;1.30.16 -y</li>
<li>conda install -c conda-forge r-devtools&#x3D;2.4.3 -y</li>
<li>conda install -c conda-forge –strict-channel-priority r-arrow&#x3D;7.0.0 -y</li>
<li>conda install -c bioconda bioconductor-aucell&#x3D;1.16.0 -y</li>
<li>conda install -c bioconda bioconductor-rcistarget -y</li>
<li>conda install -c bioconda bioconductor-complexheatmap&#x3D;2.10.0 -y</li>
<li>conda install -c bioconda bioconductor-genie3&#x3D;1.16.0 -y</li>
<li>conda install -c bioconda bioconductor-biocparallel&#x3D;1.28.3 -y</li>
<li>conda install -c conda-forge r-doparallel&#x3D;1.0.17 -y</li>
<li>conda install -c conda-forge parallel&#x3D;20220222 -y</li>
<li>conda install -c conda-forge r-foreach&#x3D;1.5.2 -y</li>
<li>conda install -c maximinio r-scopeloomr&#x3D;0.3.1 -y</li>
<li>conda install -c conda-forge r-rbokeh&#x3D;0.5.2 -y</li>
<li>conda install -c conda-forge r-nmf&#x3D;0.21.0 -y</li>
<li>wget <a target="_blank" rel="noopener" href="https://github.com/aertslab/SCENIC/archive/refs/heads/master.zip">https://github.com/aertslab/SCENIC/archive/refs/heads/master.zip</a> -O SCENIC-master.zip</li>
<li>BiocManager::install(c(“NMF”, “R2HTML”))</li>
<li>BiocManager::install(c(“doMC”, “doRNG”))</li>
<li>devtools::install_local(“SCENIC-master.zip”)</li>
<li>IRkernel::installspec(name&#x3D;’scenic’, displayname&#x3D;’r-scenic’)</li>
</ul>
<figure class="highlight shell"><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></pre></td><td class="code"><pre><code class="hljs shell">mkdir RcisTarget_data &amp;&amp; cd RcisTarget_data<br>mkdir human &amp;&amp; cd human<br>wget https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg19/refseq_r45/mc9nr/gene_based/hg19-500bp-upstream-7species.mc9nr.feather<br>wget https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg19/refseq_r45/mc9nr/gene_based/hg19-tss-centered-10kb-7species.mc9nr.feather<br><br>wget https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg38/refseq_r80/mc9nr/gene_based/hg38__refseq-r80__10kb_up_and_down_tss.mc9nr.feather<br>wget https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg38/refseq_r80/mc9nr/gene_based/hg38__refseq-r80__500bp_up_and_100bp_down_tss.mc9nr.feather<br></code></pre></td></tr></table></figure>

<p><a target="_blank" rel="noopener" href="https://www.zhihu.com/question/317951769/answer/1451116214">总体来说，hg38相对于 hg19是一个巨大进步</a>。by <a target="_blank" rel="noopener" href="https://www.zhihu.com/people/csyk2">员炊事</a></p>
<ol>
<li><strong>改变了之前的一些测序错误，组装错误</strong>。直观的例子有 degenerate bases 少了很多。</li>
<li><strong>补上了hg19中的很多gap</strong>。 特别重要的是 centromere 的序列也不再是空白。hg19的时候，centromere 的部分直接就是gap， hg38后，开始有了 a-satellitle sequences。尽管只是“简单”的表现了 a-satellite repeats， 已经是一个巨大的提升。</li>
<li>sequence 改了之后，<strong>相应的 annotation 也改了很多</strong>。比较宏观的就是 hg38 的 exome 比hg19 的大了不少。如果我的记忆没出错的话，大了25% 左右。</li>
</ol>
<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br></pre></td><td class="code"><pre><code class="hljs r">dbs <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span>`<span class="hljs-number">500</span>bp`=&#x27;hg38__refseq-r80__500bp_up_and_100bp_down_tss.mc9nr.feather&#x27;, `10kb`=&#x27;hg38__refseq-r80__10kb_up_and_down_tss.mc9nr.feather&#x27;)<br>scenicOptions &lt;- initializeScenic(org=&quot;hgnc&quot;, dbDir=&quot;~/upload/zl_liu/RcisTarget_data/human/&quot;, nCores=10, dbs = dbs)<br></code></pre></td></tr></table></figure>

<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">library<span class="hljs-punctuation">(</span>foreach<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>parallel<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>doParallel<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>BiocParallel<span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
                
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