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  133. <h1 id="seo-header">通过conda安装纯净环境的TCGAbiolinks</h1>
  134. <div class="markdown-body">
  135. <ul>
  136. <li><p>conda create -n tcga -c conda-forge r-base&#x3D;4.1.2 -y</p>
  137. </li>
  138. <li><p>conda activate tcga</p>
  139. </li>
  140. <li><p>conda install -c conda-forge r-rvest&#x3D;1.0.2 -y</p>
  141. </li>
  142. <li><p>conda install -c conda-forge r-xml&#x3D;3.99_0.8 -y</p>
  143. </li>
  144. <li><p>conda install -c conda-forge r-rcpparmadillo&#x3D;0.10.8.1.0 -y</p>
  145. </li>
  146. <li><p>conda install -c conda-forge r-bh&#x3D;1.78.0_0 -y</p>
  147. </li>
  148. <li><p>conda install -c conda-forge r-biocmanager&#x3D;1.30.16 -y</p>
  149. </li>
  150. <li><p>conda install -c bioconda bioconductor-summarizedexperiment&#x3D;1.24.0 -y</p>
  151. </li>
  152. <li><p>conda install -c bioconda bioconductor-tcgabiolinks&#x3D;2.22.1 -y</p>
  153. </li>
  154. <li><p>conda install -c bioconda bioconductor-deseq2&#x3D;1.34.0 -y</p>
  155. </li>
  156. <li><p>conda install -c bioconda bioconductor-rhdf5&#x3D;2.38.0 -y</p>
  157. </li>
  158. <li><p>conda install -c bioconda bioconductor-limma&#x3D;3.50.1 -y</p>
  159. </li>
  160. <li><p>conda install -c bioconda bioconductor-apeglm&#x3D;1.16.0 -y</p>
  161. </li>
  162. <li><p>conda install -c bioconda r-sleuth&#x3D;0.30.0 -y</p>
  163. </li>
  164. <li><p>conda install -c bioconda r-wasabi&#x3D;1.0.1 -y</p>
  165. </li>
  166. <li><p>conda install -c conda-forge r-irkernel&#x3D;1.3 -y</p>
  167. </li>
  168. <li><p>conda install -c conda-forge r-ashr&#x3D;2.2_54 -y</p>
  169. </li>
  170. <li><p>conda install -c conda-forge r-robustrankaggreg&#x3D;1.1 -y</p>
  171. </li>
  172. <li><p>conda install -c conda-forge r-devtools&#x3D;2.4.3 -y</p>
  173. </li>
  174. <li><p>IRkernel::installspec(name&#x3D;’tcga’, displayname&#x3D;’r-tcga’)</p>
  175. </li>
  176. <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>
  177. </li>
  178. <li><p>sleuth 数据要求:<strong>Kallisto</strong>输出的结果</p>
  179. </li>
  180. <li><p>limma 数据要求:logCPM;假定正态分布;适合芯片数据</p>
  181. </li>
  182. <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>
  183. </li>
  184. <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>
  185. </li>
  186. <li><p>多数据集结果整合:RobustRankAggreg</p>
  187. </li>
  188. </ul>
  189. <p>fpkm转tpm示例(基于 SummarizedExperiment 数据框架)</p>
  190. <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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