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            <h1 id="seo-header">通过conda安装纯净环境的TCGAbiolinks</h1>
            
            
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                <ul>
<li><p>conda create -n tcga -c conda-forge r-base&#x3D;4.1.2 -y</p>
</li>
<li><p>conda activate tcga</p>
</li>
<li><p>conda install -c conda-forge r-rvest&#x3D;1.0.2 -y</p>
</li>
<li><p>conda install -c conda-forge r-xml&#x3D;3.99_0.8 -y</p>
</li>
<li><p>conda install -c conda-forge r-rcpparmadillo&#x3D;0.10.8.1.0 -y</p>
</li>
<li><p>conda install -c conda-forge r-bh&#x3D;1.78.0_0 -y</p>
</li>
<li><p>conda install -c conda-forge r-biocmanager&#x3D;1.30.16 -y</p>
</li>
<li><p>conda install -c bioconda bioconductor-summarizedexperiment&#x3D;1.24.0 -y</p>
</li>
<li><p>conda install -c bioconda bioconductor-tcgabiolinks&#x3D;2.22.1 -y</p>
</li>
<li><p>conda install -c bioconda bioconductor-deseq2&#x3D;1.34.0 -y</p>
</li>
<li><p>conda install -c bioconda bioconductor-rhdf5&#x3D;2.38.0 -y</p>
</li>
<li><p>conda install -c bioconda bioconductor-limma&#x3D;3.50.1 -y</p>
</li>
<li><p>conda install -c bioconda bioconductor-apeglm&#x3D;1.16.0 -y</p>
</li>
<li><p>conda install -c bioconda r-sleuth&#x3D;0.30.0 -y</p>
</li>
<li><p>conda install -c bioconda r-wasabi&#x3D;1.0.1 -y</p>
</li>
<li><p>conda install -c conda-forge r-irkernel&#x3D;1.3 -y</p>
</li>
<li><p>conda install -c conda-forge r-ashr&#x3D;2.2_54 -y</p>
</li>
<li><p>conda install -c conda-forge r-robustrankaggreg&#x3D;1.1 -y</p>
</li>
<li><p>conda install -c conda-forge r-devtools&#x3D;2.4.3 -y</p>
</li>
<li><p>IRkernel::installspec(name&#x3D;’tcga’, displayname&#x3D;’r-tcga’)</p>
</li>
<li><p>deseq2 数据要求：低生物学重复 &amp; raw counts；假定负二项分布；适合高通量测序数据</p>
</li>
<li><p>sleuth 数据要求：<strong>Kallisto</strong>输出的结果</p>
</li>
<li><p>limma 数据要求：logCPM；假定正态分布；适合芯片数据</p>
</li>
<li><p><a target="_blank" rel="noopener" href="https://bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf">fpkm数据差异基因分析</a> ：理论上是不能进行分析的，无计可施时可以参考</p>
</li>
<li><p>高生物学重复请直接使用 <strong>wilcox.test</strong> 以避免大量假阳性</p>
</li>
<li><p>多数据集结果整合：RobustRankAggreg</p>
</li>
</ul>
<p>fpkm转tpm示例（基于 SummarizedExperiment 数据框架）</p>
<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></pre></td><td class="code"><pre><code class="hljs r">fpkmToTpm <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>fpkm<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    <span class="hljs-built_in">exp</span><span class="hljs-punctuation">(</span><span class="hljs-built_in">log</span><span class="hljs-punctuation">(</span>fpkm<span class="hljs-punctuation">)</span> <span class="hljs-operator">-</span> <span class="hljs-built_in">log</span><span class="hljs-punctuation">(</span><span class="hljs-built_in">sum</span><span class="hljs-punctuation">(</span>fpkm<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> <span class="hljs-built_in">log</span><span class="hljs-punctuation">(</span><span class="hljs-number">1e6</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br>f_fpkmToTpm <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>l_e<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>     apply<span class="hljs-punctuation">(</span>l_e<span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span>fpkmToTpm<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br>assay<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;TPM&quot;</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> f_fpkmToTpm<span class="hljs-punctuation">(</span>assay<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;HTSeq - FPKM&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
                
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