Mercurial > repos > rnateam > rbpbench

comparison test-data/report.rbpbench_compare.test.html @ 0:7dd2835ce566 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:7dd2835ce566
1 <p><head>
2 <title>RBPBench - Motif Search Comparison Report</title></p>
3 <script src="/home/malong/miniconda3/envs/rbpbench/lib/python3.9/site-packages/rbpbench/content/sorttable.js" type="text/javascript"></script>
4 <p></head></p>
5 <h1>Comparison Report</h1>
6 <p>List of available comparison statistics generated
7 by RBPBench (rbpbench compare):</p>
8 <ul>
9 <li><a href="#method-tab-1">k562_eclip,human_v0.1,PUM1 method comparison table</a></li>
10 <li><a href="#method-tab-2">k562_eclip,human_v0.1,PUM2 method comparison table</a></li>
11 <li><a href="#method-venn-1">k562_eclip,human_v0.1,PUM1 method comparison plot</a></li>
12 <li><a href="#method-venn-2">k562_eclip,human_v0.1,PUM2 method comparison plot</a></li>
13 </ul>
14 <p>&nbsp;</p>
15 <h2 id="method-tab-1">k562_eclip,human_v0.1,PUM1 method comparison statistics</h2>
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>
17 <table class="sortable">
18 <thead>
19 <tr>
20 <th style="text-align: center;">Method ID</th>
21 <th style="text-align: center;"># regions</th>
22 <th style="text-align: center;"># motif hits</th>
23 <th style="text-align: center;">% regions with motifs</th>
24 <th style="text-align: center;">% motif nucleotides</th>
25 <th style="text-align: center;"># motif hits per 1000 nt</th>
26 </tr>
27 </thead>
28 <tbody>
29 <tr>
30 <td style="text-align: center;">dewseq_w100_s5</td>
31 <td style="text-align: center;">23</td>
32 <td style="text-align: center;">24</td>
33 <td style="text-align: center;">43.48</td>
34 <td style="text-align: center;">3.20</td>
35 <td style="text-align: center;">4.86</td>
36 </tr>
37 <tr>
38 <td style="text-align: center;">clipper_idr</td>
39 <td style="text-align: center;">32</td>
40 <td style="text-align: center;">8</td>
41 <td style="text-align: center;">18.75</td>
42 <td style="text-align: center;">2.69</td>
43 <td style="text-align: center;">3.84</td>
44 </tr>
45 </tbody>
46 </table>
47 <p>&nbsp;
48 &nbsp;</p>
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>
50 <h2 id="method-tab-2">k562_eclip,human_v0.1,PUM2 method comparison statistics</h2>
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>
52 <table class="sortable">
53 <thead>
54 <tr>
55 <th style="text-align: center;">Method ID</th>
56 <th style="text-align: center;"># regions</th>
57 <th style="text-align: center;"># motif hits</th>
58 <th style="text-align: center;">% regions with motifs</th>
59 <th style="text-align: center;">% motif nucleotides</th>
60 <th style="text-align: center;"># motif hits per 1000 nt</th>
61 </tr>
62 </thead>
63 <tbody>
64 <tr>
65 <td style="text-align: center;">dewseq_w100_s5</td>
66 <td style="text-align: center;">70</td>
67 <td style="text-align: center;">448</td>
68 <td style="text-align: center;">92.86</td>
69 <td style="text-align: center;">14.08</td>
70 <td style="text-align: center;">31.46</td>
71 </tr>
72 <tr>
73 <td style="text-align: center;">clipper_idr</td>
74 <td style="text-align: center;">77</td>
75 <td style="text-align: center;">219</td>
76 <td style="text-align: center;">76.62</td>
77 <td style="text-align: center;">17.64</td>
78 <td style="text-align: center;">46.89</td>
79 </tr>
80 </tbody>
81 </table>
82 <p>&nbsp;
83 &nbsp;</p>
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>
85 <h2 id="method-venn-1">k562_eclip,human_v0.1,PUM1 method comparison plot</h2>
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.
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>
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
89 title="dataset comparison plot k562_eclip,human_v0.1,PUM1" width="700" /></p>
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>
91 <p>&nbsp;</p>
92 <h2 id="method-venn-2">k562_eclip,human_v0.1,PUM2 method comparison plot</h2>
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.
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>
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
96 title="dataset comparison plot k562_eclip,human_v0.1,PUM2" width="700" /></p>
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>
98 <p>&nbsp;</p>