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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench commit 0e21bd630200c1f199db8ba5d83b81d4214fc59f
author rnateam
date Sun, 03 Dec 2023 12:51:54 +0000
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7dd2835ce566 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench commit 0e21bd630200c1f199db8ba5d83b81d4214fc59f
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1 <p><head>
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2 <title>RBPBench - Motif Search Comparison Report</title></p>
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3 <script src="/home/malong/miniconda3/envs/rbpbench/lib/python3.9/site-packages/rbpbench/content/sorttable.js" type="text/javascript"></script>
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4 <p></head></p>
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5 <h1>Comparison Report</h1>
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6 <p>List of available comparison statistics generated
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7 by RBPBench (rbpbench compare):</p>
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8 <ul>
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9 <li><a href="#method-tab-1">k562_eclip,human_v0.1,PUM1 method comparison table</a></li>
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10 <li><a href="#method-tab-2">k562_eclip,human_v0.1,PUM2 method comparison table</a></li>
7dd2835ce566 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench commit 0e21bd630200c1f199db8ba5d83b81d4214fc59f
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11 <li><a href="#method-venn-1">k562_eclip,human_v0.1,PUM1 method comparison plot</a></li>
7dd2835ce566 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench commit 0e21bd630200c1f199db8ba5d83b81d4214fc59f
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12 <li><a href="#method-venn-2">k562_eclip,human_v0.1,PUM2 method comparison plot</a></li>
7dd2835ce566 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench commit 0e21bd630200c1f199db8ba5d83b81d4214fc59f
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13 </ul>
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14 <p>&nbsp;</p>
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15 <h2 id="method-tab-1">k562_eclip,human_v0.1,PUM1 method comparison statistics</h2>
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16 <p><strong>Table:</strong> RBP motif hit statistics for combined ID "k562_eclip,human_v0.1,PUM1" (data ID, motif database ID, RBP ID) over different methods (method ID column).</p>
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17 <table class="sortable">
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18 <thead>
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19 <tr>
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20 <th style="text-align: center;">Method ID</th>
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21 <th style="text-align: center;"># regions</th>
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22 <th style="text-align: center;"># motif hits</th>
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23 <th style="text-align: center;">% regions with motifs</th>
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24 <th style="text-align: center;">% motif nucleotides</th>
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25 <th style="text-align: center;"># motif hits per 1000 nt</th>
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26 </tr>
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27 </thead>
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28 <tbody>
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29 <tr>
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30 <td style="text-align: center;">dewseq_w100_s5</td>
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31 <td style="text-align: center;">23</td>
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32 <td style="text-align: center;">24</td>
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33 <td style="text-align: center;">43.48</td>
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34 <td style="text-align: center;">3.20</td>
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35 <td style="text-align: center;">4.86</td>
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36 </tr>
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37 <tr>
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38 <td style="text-align: center;">clipper_idr</td>
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39 <td style="text-align: center;">32</td>
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40 <td style="text-align: center;">8</td>
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41 <td style="text-align: center;">18.75</td>
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42 <td style="text-align: center;">2.69</td>
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43 <td style="text-align: center;">3.84</td>
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44 </tr>
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45 </tbody>
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46 </table>
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47 <p>&nbsp;
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48 &nbsp;</p>
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49 <p>Column IDs have the following meanings: <strong>Method ID</strong> -&gt; method ID set for dataset (typically peak calling method ID), <strong># regions</strong> -&gt; number of peak regions used for motif search, <strong># motif hits</strong> -&gt; number of unique motif hits in peak regions (removed double counts), <strong>% regions with motifs</strong> -&gt; percentage of peak regions with motif hits, <strong>% motif nucleotides</strong> -&gt; percentage of unique motif nucleotides over effective peak region size (overlapping regions merged), <strong># motif hits per 1000 nt</strong> -&gt; number of motif hits over 1000 nt of called peak region size (overlapping regions NOT merged).</p>
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50 <h2 id="method-tab-2">k562_eclip,human_v0.1,PUM2 method comparison statistics</h2>
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51 <p><strong>Table:</strong> RBP motif hit statistics for combined ID "k562_eclip,human_v0.1,PUM2" (data ID, motif database ID, RBP ID) over different methods (method ID column).</p>
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52 <table class="sortable">
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53 <thead>
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54 <tr>
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55 <th style="text-align: center;">Method ID</th>
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56 <th style="text-align: center;"># regions</th>
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57 <th style="text-align: center;"># motif hits</th>
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58 <th style="text-align: center;">% regions with motifs</th>
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59 <th style="text-align: center;">% motif nucleotides</th>
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60 <th style="text-align: center;"># motif hits per 1000 nt</th>
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61 </tr>
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62 </thead>
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63 <tbody>
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64 <tr>
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65 <td style="text-align: center;">dewseq_w100_s5</td>
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66 <td style="text-align: center;">70</td>
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67 <td style="text-align: center;">448</td>
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68 <td style="text-align: center;">92.86</td>
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69 <td style="text-align: center;">14.08</td>
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70 <td style="text-align: center;">31.46</td>
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71 </tr>
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72 <tr>
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73 <td style="text-align: center;">clipper_idr</td>
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74 <td style="text-align: center;">77</td>
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75 <td style="text-align: center;">219</td>
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76 <td style="text-align: center;">76.62</td>
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77 <td style="text-align: center;">17.64</td>
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78 <td style="text-align: center;">46.89</td>
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79 </tr>
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80 </tbody>
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81 </table>
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82 <p>&nbsp;
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83 &nbsp;</p>
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84 <p>Column IDs have the following meanings: <strong>Method ID</strong> -&gt; method ID set for dataset (typically peak calling method ID), <strong># regions</strong> -&gt; number of peak regions used for motif search, <strong># motif hits</strong> -&gt; number of unique motif hits in peak regions (removed double counts), <strong>% regions with motifs</strong> -&gt; percentage of peak regions with motif hits, <strong>% motif nucleotides</strong> -&gt; percentage of unique motif nucleotides over effective peak region size (overlapping regions merged), <strong># motif hits per 1000 nt</strong> -&gt; number of motif hits over 1000 nt of called peak region size (overlapping regions NOT merged).</p>
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85 <h2 id="method-venn-1">k562_eclip,human_v0.1,PUM1 method comparison plot</h2>
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86 <p>Based on the same combined ID "k562_eclip,human_v0.1,PUM1" (data ID, motif database ID, RBP ID), motif hit occurrences for 2 different methods (clipper_idr,dewseq_w100_s5) are compared via Venn diagram.
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87 Any given motif hit can either be found only by one method, or be identified by any set (&gt;=2) of methods (intersection areas).</p>
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88 <p><img src="html_report_plots/venn_diagram.method_comp.k562_eclip,human_v0.1,PUM1.png" alt="dataset comparison plot k562_eclip,human_v0.1,PUM1
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89 title="dataset comparison plot k562_eclip,human_v0.1,PUM1" width="700" /></p>
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90 <p><strong>Figure:</strong> Venn diagram of motif hit occurrences for 2 different methods (clipper_idr,dewseq_w100_s5) with identical combined ID (k562_eclip,human_v0.1,PUM1) + corresponding percentages of total motif hits for each region (method exclusive and intersection(s)).</p>
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91 <p>&nbsp;</p>
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92 <h2 id="method-venn-2">k562_eclip,human_v0.1,PUM2 method comparison plot</h2>
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93 <p>Based on the same combined ID "k562_eclip,human_v0.1,PUM2" (data ID, motif database ID, RBP ID), motif hit occurrences for 2 different methods (clipper_idr,dewseq_w100_s5) are compared via Venn diagram.
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94 Any given motif hit can either be found only by one method, or be identified by any set (&gt;=2) of methods (intersection areas).</p>
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95 <p><img src="html_report_plots/venn_diagram.method_comp.k562_eclip,human_v0.1,PUM2.png" alt="dataset comparison plot k562_eclip,human_v0.1,PUM2
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96 title="dataset comparison plot k562_eclip,human_v0.1,PUM2" width="700" /></p>
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97 <p><strong>Figure:</strong> Venn diagram of motif hit occurrences for 2 different methods (clipper_idr,dewseq_w100_s5) with identical combined ID (k562_eclip,human_v0.1,PUM2) + corresponding percentages of total motif hits for each region (method exclusive and intersection(s)).</p>
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98 <p>&nbsp;</p>