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<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
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<meta charset="utf-8">
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<div class="fluid-row" id="header">
</div>
<div id="TOC">
<ul>
<li><a href="#sample-report">Sample report</a><ul>
<li><a href="#overview">Overview</a><ul>
<li><a href="#generate-alignment-report">Generate alignment report</a></li>
<li><a href="#checking-the-consistency-between-replicates">Checking the consistency between replicates</a></li>
</ul></li>
</ul></li>
</ul>
</div>
<div id="sample-report" class="section level1">
<h1>Sample report</h1>
<p><strong>Author:</strong> <a href="mailto:[email protected]">Wanqing Shao</a></p>
<p><strong>Generated:</strong> Fri Apr 07 2017, 05:35 PM</p>
<div id="overview" class="section level2">
<h2>Overview</h2>
<p>Generate alignment report, report contains raw sequencing reads, reads containing fixed barcode (only applicable to ChIP-nexus samples), aligned reads and uniquely aligned reads. If two replicates were performed, calculate R2 values between replicates by performing linear regression on the read counts that fall within each mRNA promoter region.</p>
<div id="generate-alignment-report" class="section level3">
<h3>Generate alignment report</h3>
<table style="width:100%;">
<caption>alignment report</caption>
<colgroup>
<col width="46%" />
<col width="11%" />
<col width="10%" />
<col width="15%" />
<col width="16%" />
</colgroup>
<thead>
<tr class="header">
<th align="center">sample</th>
<th align="center">raw_reads</th>
<th align="center">pf_reads</th>
<th align="center">aligned_reads</th>
<th align="center">uniquely_aligned</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center">kc167_dmso_polii_chipnexus_1</td>
<td align="center">51506284</td>
<td align="center">45260709</td>
<td align="center">32713360</td>
<td align="center">31687336</td>
</tr>
<tr class="even">
<td align="center">kc167_dmso_polii_chipnexus_2</td>
<td align="center">44474257</td>
<td align="center">39421854</td>
<td align="center">27226774</td>
<td align="center">26515507</td>
</tr>
<tr class="odd">
<td align="center">kc167_dmso_taf2_chipnexus_1</td>
<td align="center">27615761</td>
<td align="center">26099296</td>
<td align="center">11935966</td>
<td align="center">8867953</td>
</tr>
<tr class="even">
<td align="center">kc167_dmso_taf2_chipnexus_2</td>
<td align="center">69474222</td>
<td align="center">60378714</td>
<td align="center">37182953</td>
<td align="center">35118131</td>
</tr>
<tr class="odd">
<td align="center">kc167_dmso_tbp_chipnexus_1</td>
<td align="center">34308181</td>
<td align="center">31562031</td>
<td align="center">19482290</td>
<td align="center">17021565</td>
</tr>
<tr class="even">
<td align="center">kc167_dmso_tbp_chipnexus_2</td>
<td align="center">42035326</td>
<td align="center">39877758</td>
<td align="center">2.4e+07</td>
<td align="center">8637932</td>
</tr>
<tr class="odd">
<td align="center">kc167_dmso_tfiia_chipnexus_1</td>
<td align="center">88390232</td>
<td align="center">77035411</td>
<td align="center">46390877</td>
<td align="center">41107057</td>
</tr>
<tr class="even">
<td align="center">kc167_dmso_tfiia_chipnexus_2</td>
<td align="center">61060678</td>
<td align="center">53756202</td>
<td align="center">33282489</td>
<td align="center">30902354</td>
</tr>
<tr class="odd">
<td align="center">kc167_dmso_tfiib_chipnexus_1</td>
<td align="center">39193769</td>
<td align="center">36468644</td>
<td align="center">25343480</td>
<td align="center">21360921</td>
</tr>
<tr class="even">
<td align="center">kc167_dmso_tfiib_chipnexus_2</td>
<td align="center">41159305</td>
<td align="center">38774942</td>
<td align="center">24720185</td>
<td align="center">14087637</td>
</tr>
<tr class="odd">
<td align="center">kc167_dmso_tfiif_chipnexus_1</td>
<td align="center">26034300</td>
<td align="center">25055941</td>
<td align="center">12644852</td>
<td align="center">6490679</td>
</tr>
<tr class="even">
<td align="center">kc167_dmso_tfiif_chipnexus_2</td>
<td align="center">38546116</td>
<td align="center">36513377</td>
<td align="center">19961712</td>
<td align="center">7163041</td>
</tr>
<tr class="odd">
<td align="center">kc167_dmso_xpb_chipnexus_1</td>
<td align="center">27444816</td>
<td align="center">26410482</td>
<td align="center">15462556</td>
<td align="center">7258046</td>
</tr>
<tr class="even">
<td align="center">kc167_dmso_xpb_chipnexus_2</td>
<td align="center">41379406</td>
<td align="center">39594430</td>
<td align="center">24960938</td>
<td align="center">8661151</td>
</tr>
<tr class="odd">
<td align="center">kc167_triptolide_polii_chipnexus_1</td>
<td align="center">25151875</td>
<td align="center">24005461</td>
<td align="center">16164911</td>
<td align="center">11275865</td>
</tr>
<tr class="even">
<td align="center">kc167_triptolide_polii_chipnexus_2</td>
<td align="center">34586183</td>
<td align="center">31339389</td>
<td align="center">14660565</td>
<td align="center">11052892</td>
</tr>
<tr class="odd">
<td align="center">kc167_triptolide_taf2_chipnexus_1</td>
<td align="center">28472379</td>
<td align="center">27228243</td>
<td align="center">15154299</td>
<td align="center">7464603</td>
</tr>
<tr class="even">
<td align="center">kc167_triptolide_taf2_chipnexus_2</td>
<td align="center">39566435</td>
<td align="center">37884448</td>
<td align="center">21778231</td>
<td align="center">17008792</td>
</tr>
<tr class="odd">
<td align="center">kc167_triptolide_tbp_chipnexus_1</td>
<td align="center">17083794</td>
<td align="center">16095381</td>
<td align="center">9642493</td>
<td align="center">5567671</td>
</tr>
<tr class="even">
<td align="center">kc167_triptolide_tbp_chipnexus_2</td>
<td align="center">36319496</td>
<td align="center">32253370</td>
<td align="center">20700891</td>
<td align="center">11413966</td>
</tr>
<tr class="odd">
<td align="center">kc167_triptolide_tfiia_chipnexus_1</td>
<td align="center">27572472</td>
<td align="center">25187368</td>
<td align="center">14072528</td>
<td align="center">9647929</td>
</tr>
<tr class="even">
<td align="center">kc167_triptolide_tfiia_chipnexus_2</td>
<td align="center">46781726</td>
<td align="center">40839904</td>
<td align="center">18379739</td>
<td align="center">12453994</td>
</tr>
<tr class="odd">
<td align="center">kc167_triptolide_tfiib_chipnexus_1</td>
<td align="center">36982177</td>
<td align="center">34554109</td>
<td align="center">24627955</td>
<td align="center">22345288</td>
</tr>
<tr class="even">
<td align="center">kc167_triptolide_tfiib_chipnexus_2</td>
<td align="center">27606088</td>
<td align="center">24794568</td>
<td align="center">13078465</td>
<td align="center">10595177</td>
</tr>
<tr class="odd">
<td align="center">kc167_triptolide_tfiif_chipnexus_1</td>
<td align="center">24013530</td>
<td align="center">23163379</td>
<td align="center">16992900</td>
<td align="center">9223448</td>
</tr>
<tr class="even">
<td align="center">kc167_triptolide_tfiif_chipnexus_2</td>
<td align="center">24134703</td>
<td align="center">22625711</td>
<td align="center">9927555</td>
<td align="center">6310976</td>
</tr>
<tr class="odd">
<td align="center">kc167_triptolide_xpb_chipnexus_1</td>
<td align="center">26411031</td>
<td align="center">25310595</td>
<td align="center">17284283</td>
<td align="center">7609049</td>
</tr>
<tr class="even">
<td align="center">kc167_triptolide_xpb_chipnexus_2</td>
<td align="center">26340308</td>
<td align="center">23673096</td>
<td align="center">1.5e+07</td>
<td align="center">5357934</td>
</tr>
<tr class="odd">
<td align="center">kc167_dmso_control_polii_chipnexus_spikein_1</td>
<td align="center">50367225</td>
<td align="center">45323642</td>
<td align="center">33489001</td>
<td align="center">32839969</td>
</tr>
<tr class="even">
<td align="center">kc167_dmso_control_polii_chipnexus_spikein_2</td>
<td align="center">60753874</td>
<td align="center">54225842</td>
<td align="center">41182813</td>
<td align="center">40493567</td>
</tr>
<tr class="odd">
<td align="center">kc167_triptolide_10min_polii_chipnexus_spikein_1</td>
<td align="center">39789783</td>
<td align="center">35461605</td>
<td align="center">27201115</td>
<td align="center">26814567</td>
</tr>
<tr class="even">
<td align="center">kc167_triptolide_10min_polii_chipnexus_spikein_2</td>
<td align="center">20140681</td>
<td align="center">17722095</td>
<td align="center">13273738</td>
<td align="center">13137715</td>
</tr>
<tr class="odd">
<td align="center">kc167_triptolide_20min_polii_chipnexus_spikein_1</td>
<td align="center">34276369</td>
<td align="center">30565199</td>
<td align="center">23080308</td>
<td align="center">22765757</td>
</tr>
<tr class="even">
<td align="center">kc167_triptolide_20min_polii_chipnexus_spikein_2</td>
<td align="center">21374089</td>
<td align="center">18833981</td>
<td align="center">14227691</td>
<td align="center">14022077</td>
</tr>
<tr class="odd">
<td align="center">kc167_triptolide_30min_polii_chipnexus_spikein_1</td>
<td align="center">76515727</td>
<td align="center">69112612</td>
<td align="center">52153638</td>
<td align="center">50552565</td>
</tr>
<tr class="even">
<td align="center">kc167_triptolide_30min_polii_chipnexus_spikein_2</td>
<td align="center">31483045</td>
<td align="center">27281495</td>
<td align="center">20475458</td>
<td align="center">20229156</td>
</tr>
<tr class="odd">
<td align="center">kc167_triptolide_5min_polii_chipnexus_spikein_1</td>
<td align="center">40241894</td>
<td align="center">35713917</td>
<td align="center">27050367</td>
<td align="center">26644102</td>
</tr>
<tr class="even">
<td align="center">kc167_triptolide_5min_polii_chipnexus_spikein_2</td>
<td align="center">23485160</td>
<td align="center">20791751</td>
<td align="center">15509479</td>
<td align="center">15310124</td>
</tr>
<tr class="odd">
<td align="center">kc167_polii_chipnexus</td>
<td align="center">13525362</td>
<td align="center">12715019</td>
<td align="center">7325429</td>
<td align="center">7093645</td>
</tr>
<tr class="even">
<td align="center">kc167_tfiia_chipnexus</td>
<td align="center">25645488</td>
<td align="center">23803415</td>
<td align="center">7502727</td>
<td align="center">6788185</td>
</tr>
<tr class="odd">
<td align="center">kc167_tfiib_chipnexus</td>
<td align="center">21212724</td>
<td align="center">19730637</td>
<td align="center">6327593</td>
<td align="center">5642160</td>
</tr>
<tr class="even">
<td align="center">kc167_polii_chipseq</td>
<td align="center">6637677</td>
<td align="center">NA</td>
<td align="center">5332672</td>
<td align="center">5330874</td>
</tr>
<tr class="odd">
<td align="center">kc167_tfiia_chipseq</td>
<td align="center">10706947</td>
<td align="center">NA</td>
<td align="center">7404586</td>
<td align="center">7381185</td>
</tr>
<tr class="even">
<td align="center">kc167_tfiib_chipseq</td>
<td align="center">44828488</td>
<td align="center">NA</td>
<td align="center">33036231</td>
<td align="center">32282841</td>
</tr>
<tr class="odd">
<td align="center">kc167_dmso_nelfe_chipnexus_1</td>
<td align="center">66055484</td>
<td align="center">5.7e+07</td>
<td align="center">42399566</td>
<td align="center">39331570</td>
</tr>
<tr class="even">
<td align="center">kc167_dmso_nelfe_chipnexus_2</td>
<td align="center">28142735</td>
<td align="center">23536842</td>
<td align="center">17738145</td>
<td align="center">10858968</td>
</tr>
<tr class="odd">
<td align="center">kc167_triptolide_nelfe_chipnexus_1</td>
<td align="center">55779413</td>
<td align="center">48276164</td>
<td align="center">35675575</td>
<td align="center">32467972</td>
</tr>
<tr class="even">
<td align="center">kc167_triptolide_nelfe_chipnexus_2</td>
<td align="center">38249409</td>
<td align="center">33232813</td>
<td align="center">22865361</td>
<td align="center">20915091</td>
</tr>
<tr class="odd">
<td align="center">kc167_triptolide_0.5um_polii_chipnexus</td>
<td align="center">49030340</td>
<td align="center">42695991</td>
<td align="center">31077220</td>
<td align="center">29696794</td>
</tr>
<tr class="even">
<td align="center">kc167_triptolide_500um_polii_chipnexus</td>
<td align="center">51923487</td>
<td align="center">45529516</td>
<td align="center">32582129</td>
<td align="center">31038178</td>
</tr>
<tr class="odd">
<td align="center">kc167_flavopiridol_0.5um_polii_chipnexus_1</td>
<td align="center">41718789</td>
<td align="center">37181319</td>
<td align="center">25324984</td>
<td align="center">24655251</td>
</tr>
<tr class="even">
<td align="center">kc167_flavopiridol_0.5um_polii_chipnexus_2</td>
<td align="center">42790057</td>
<td align="center">37488226</td>
<td align="center">26910617</td>
<td align="center">26115928</td>
</tr>
<tr class="odd">
<td align="center">kc167_drb_50um_polii_chipnexus_1</td>
<td align="center">41039480</td>
<td align="center">36619267</td>
<td align="center">24802789</td>
<td align="center">24142606</td>
</tr>
<tr class="even">
<td align="center">kc167_drb_50um_polii_chipnexus_2</td>
<td align="center">41759489</td>
<td align="center">36626314</td>
<td align="center">25788324</td>
<td align="center">25041204</td>
</tr>
<tr class="odd">
<td align="center">kc167_egfp_rnai_polii_chipnexus_spikein_1</td>
<td align="center">37314359</td>
<td align="center">33240409</td>
<td align="center">22186191</td>
<td align="center">21533884</td>
</tr>
<tr class="even">
<td align="center">kc167_egfp_rnai_polii_chipnexus_spikein_2</td>
<td align="center">62548291</td>
<td align="center">55376433</td>
<td align="center">39152973</td>
<td align="center">37850736</td>
</tr>
<tr class="odd">
<td align="center">kc167_nelfe_b_rnai_polii_chipnexus_spikein_1</td>
<td align="center">36736259</td>
<td align="center">32801900</td>
<td align="center">21589767</td>
<td align="center">20984091</td>
</tr>
<tr class="even">
<td align="center">kc167_nelfe_b_rnai_polii_chipnexus_spikein_2</td>
<td align="center">54515876</td>
<td align="center">48467638</td>
<td align="center">33346514</td>
<td align="center">32214441</td>
</tr>
<tr class="odd">
<td align="center">kc167_flavopiridol_polii_chipnexus_1</td>
<td align="center">0</td>
<td align="center">25061084</td>
<td align="center">11277952</td>
<td align="center">6781628</td>
</tr>
<tr class="even">
<td align="center">kc167_flavopiridol_polii_chipnexus_2</td>
<td align="center">0</td>
<td align="center">35491604</td>
<td align="center">16471939</td>
<td align="center">12845138</td>
</tr>
</tbody>
</table>
</div>
<div id="checking-the-consistency-between-replicates" class="section level3">
<h3>Checking the consistency between replicates</h3>
<table style="width:83%;">
<caption>consistency report</caption>
<colgroup>
<col width="68%" />
<col width="15%" />
</colgroup>
<thead>
<tr class="header">
<th align="center">sample</th>
<th align="center">r_squared</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center">kc167_dmso_polii_chipnexus_1</td>
<td align="center">0.972</td>
</tr>
<tr class="even">
<td align="center">kc167_dmso_polii_chipnexus_2</td>
<td align="center">0.972</td>
</tr>
<tr class="odd">
<td align="center">kc167_dmso_taf2_chipnexus_1</td>
<td align="center">0.944</td>
</tr>
<tr class="even">
<td align="center">kc167_dmso_taf2_chipnexus_2</td>
<td align="center">0.944</td>
</tr>
<tr class="odd">
<td align="center">kc167_dmso_tbp_chipnexus_1</td>
<td align="center">0.948</td>
</tr>
<tr class="even">
<td align="center">kc167_dmso_tbp_chipnexus_2</td>
<td align="center">0.948</td>
</tr>
<tr class="odd">
<td align="center">kc167_dmso_tfiia_chipnexus_1</td>
<td align="center">0.998</td>
</tr>
<tr class="even">
<td align="center">kc167_dmso_tfiia_chipnexus_2</td>
<td align="center">0.998</td>
</tr>
<tr class="odd">
<td align="center">kc167_dmso_tfiib_chipnexus_1</td>
<td align="center">0.869</td>
</tr>
<tr class="even">
<td align="center">kc167_dmso_tfiib_chipnexus_2</td>
<td align="center">0.869</td>
</tr>
<tr class="odd">
<td align="center">kc167_dmso_tfiif_chipnexus_1</td>
<td align="center">0.918</td>
</tr>
<tr class="even">
<td align="center">kc167_dmso_tfiif_chipnexus_2</td>
<td align="center">0.918</td>
</tr>
<tr class="odd">
<td align="center">kc167_dmso_xpb_chipnexus_1</td>
<td align="center">0.918</td>
</tr>
<tr class="even">
<td align="center">kc167_dmso_xpb_chipnexus_2</td>
<td align="center">0.918</td>
</tr>
<tr class="odd">
<td align="center">kc167_triptolide_polii_chipnexus_1</td>
<td align="center">0.888</td>
</tr>
<tr class="even">
<td align="center">kc167_triptolide_polii_chipnexus_2</td>
<td align="center">0.888</td>
</tr>
<tr class="odd">
<td align="center">kc167_triptolide_taf2_chipnexus_1</td>
<td align="center">0.956</td>
</tr>
<tr class="even">
<td align="center">kc167_triptolide_taf2_chipnexus_2</td>
<td align="center">0.956</td>
</tr>
<tr class="odd">
<td align="center">kc167_triptolide_tbp_chipnexus_1</td>
<td align="center">0.911</td>
</tr>
<tr class="even">
<td align="center">kc167_triptolide_tbp_chipnexus_2</td>
<td align="center">0.911</td>
</tr>
<tr class="odd">
<td align="center">kc167_triptolide_tfiia_chipnexus_1</td>
<td align="center">0.966</td>
</tr>
<tr class="even">
<td align="center">kc167_triptolide_tfiia_chipnexus_2</td>
<td align="center">0.966</td>
</tr>
<tr class="odd">
<td align="center">kc167_triptolide_tfiib_chipnexus_1</td>
<td align="center">0.943</td>
</tr>
<tr class="even">
<td align="center">kc167_triptolide_tfiib_chipnexus_2</td>
<td align="center">0.943</td>
</tr>
<tr class="odd">
<td align="center">kc167_triptolide_tfiif_chipnexus_1</td>
<td align="center">0.956</td>
</tr>
<tr class="even">
<td align="center">kc167_triptolide_tfiif_chipnexus_2</td>
<td align="center">0.956</td>
</tr>
<tr class="odd">
<td align="center">kc167_triptolide_xpb_chipnexus_1</td>
<td align="center">0.95</td>
</tr>
<tr class="even">
<td align="center">kc167_triptolide_xpb_chipnexus_2</td>
<td align="center">0.95</td>
</tr>
<tr class="odd">
<td align="center">kc167_dmso_control_polii_chipnexus_spikein_1</td>
<td align="center">0.982</td>
</tr>
<tr class="even">
<td align="center">kc167_dmso_control_polii_chipnexus_spikein_2</td>
<td align="center">0.982</td>
</tr>
<tr class="odd">
<td align="center">kc167_triptolide_10min_polii_chipnexus_spikein_1</td>
<td align="center">0.981</td>
</tr>
<tr class="even">
<td align="center">kc167_triptolide_10min_polii_chipnexus_spikein_2</td>
<td align="center">0.981</td>
</tr>
<tr class="odd">
<td align="center">kc167_triptolide_20min_polii_chipnexus_spikein_1</td>
<td align="center">0.96</td>
</tr>
<tr class="even">
<td align="center">kc167_triptolide_20min_polii_chipnexus_spikein_2</td>
<td align="center">0.96</td>
</tr>
<tr class="odd">
<td align="center">kc167_triptolide_30min_polii_chipnexus_spikein_1</td>
<td align="center">0.955</td>
</tr>
<tr class="even">
<td align="center">kc167_triptolide_30min_polii_chipnexus_spikein_2</td>
<td align="center">0.955</td>
</tr>
<tr class="odd">
<td align="center">kc167_triptolide_5min_polii_chipnexus_spikein_1</td>
<td align="center">0.979</td>
</tr>
<tr class="even">
<td align="center">kc167_triptolide_5min_polii_chipnexus_spikein_2</td>
<td align="center">0.979</td>
</tr>
<tr class="odd">
<td align="center">kc167_dmso_nelfe_chipnexus_1</td>
<td align="center">0.925</td>
</tr>
<tr class="even">
<td align="center">kc167_dmso_nelfe_chipnexus_2</td>
<td align="center">0.925</td>
</tr>
<tr class="odd">
<td align="center">kc167_triptolide_nelfe_chipnexus_1</td>
<td align="center">0.88</td>
</tr>
<tr class="even">
<td align="center">kc167_triptolide_nelfe_chipnexus_2</td>
<td align="center">0.88</td>
</tr>
<tr class="odd">
<td align="center">kc167_flavopiridol_0.5um_polii_chipnexus_1</td>
<td align="center">0.848</td>
</tr>
<tr class="even">
<td align="center">kc167_flavopiridol_0.5um_polii_chipnexus_2</td>
<td align="center">0.848</td>
</tr>
<tr class="odd">
<td align="center">kc167_drb_50um_polii_chipnexus_1</td>
<td align="center">0.966</td>
</tr>
<tr class="even">
<td align="center">kc167_drb_50um_polii_chipnexus_2</td>
<td align="center">0.966</td>
</tr>
<tr class="odd">
<td align="center">kc167_egfp_rnai_polii_chipnexus_spikein_1</td>
<td align="center">0.994</td>
</tr>
<tr class="even">
<td align="center">kc167_egfp_rnai_polii_chipnexus_spikein_2</td>
<td align="center">0.994</td>
</tr>
<tr class="odd">
<td align="center">kc167_nelfe_b_rnai_polii_chipnexus_spikein_1</td>
<td align="center">0.995</td>
</tr>
<tr class="even">
<td align="center">kc167_nelfe_b_rnai_polii_chipnexus_spikein_2</td>
<td align="center">0.995</td>
</tr>
<tr class="odd">
<td align="center">kc167_flavopiridol_polii_chipnexus_1</td>
<td align="center">0.977</td>
</tr>
<tr class="even">
<td align="center">kc167_flavopiridol_polii_chipnexus_2</td>
<td align="center">0.977</td>
</tr>
</tbody>
</table>
<pre><code>## R version 3.3.2 (2016-10-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.2 LTS
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats4 parallel stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] rtracklayer_1.32.2 digest_0.6.12
## [3] pander_0.6.0 magrittr_1.5
## [5] GenomicAlignments_1.8.4 SummarizedExperiment_1.2.3
## [7] Biobase_2.32.0 Rsamtools_1.24.0
## [9] Biostrings_2.40.2 XVector_0.12.1
## [11] GenomicRanges_1.24.3 GenomeInfoDb_1.8.7
## [13] IRanges_2.6.1 S4Vectors_0.10.3
## [15] BiocGenerics_0.18.0
##
## loaded via a namespace (and not attached):
## [1] Rcpp_0.12.9 knitr_1.15.1 zlibbioc_1.18.0 BiocParallel_1.6.6
## [5] stringr_1.2.0 tools_3.3.2 htmltools_0.3.5 yaml_2.1.14
## [9] rprojroot_1.2 bitops_1.0-6 RCurl_1.95-4.8 evaluate_0.10
## [13] rmarkdown_1.3 stringi_1.1.2 backports_1.0.5 XML_3.98-1.5</code></pre>
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