Mercurial > repos > rnateam > rbpbench
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench commit 0e21bd630200c1f199db8ba5d83b81d4214fc59f
| author | rnateam |
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| date | Sun, 03 Dec 2023 12:51:54 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/report.rbpbench_compare.test.html Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,98 @@ +<p><head> +<title>RBPBench - Motif Search Comparison Report</title></p> +<script src="/home/malong/miniconda3/envs/rbpbench/lib/python3.9/site-packages/rbpbench/content/sorttable.js" type="text/javascript"></script> +<p></head></p> +<h1>Comparison Report</h1> +<p>List of available comparison statistics generated +by RBPBench (rbpbench compare):</p> +<ul> +<li><a href="#method-tab-1">k562_eclip,human_v0.1,PUM1 method comparison table</a></li> +<li><a href="#method-tab-2">k562_eclip,human_v0.1,PUM2 method comparison table</a></li> +<li><a href="#method-venn-1">k562_eclip,human_v0.1,PUM1 method comparison plot</a></li> +<li><a href="#method-venn-2">k562_eclip,human_v0.1,PUM2 method comparison plot</a></li> +</ul> +<p> </p> +<h2 id="method-tab-1">k562_eclip,human_v0.1,PUM1 method comparison statistics</h2> +<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> +<table class="sortable"> +<thead> +<tr> +<th style="text-align: center;">Method ID</th> +<th style="text-align: center;"># regions</th> +<th style="text-align: center;"># motif hits</th> +<th style="text-align: center;">% regions with motifs</th> +<th style="text-align: center;">% motif nucleotides</th> +<th style="text-align: center;"># motif hits per 1000 nt</th> +</tr> +</thead> +<tbody> +<tr> +<td style="text-align: center;">dewseq_w100_s5</td> +<td style="text-align: center;">23</td> +<td style="text-align: center;">24</td> +<td style="text-align: center;">43.48</td> +<td style="text-align: center;">3.20</td> +<td style="text-align: center;">4.86</td> +</tr> +<tr> +<td style="text-align: center;">clipper_idr</td> +<td style="text-align: center;">32</td> +<td style="text-align: center;">8</td> +<td style="text-align: center;">18.75</td> +<td style="text-align: center;">2.69</td> +<td style="text-align: center;">3.84</td> +</tr> +</tbody> +</table> +<p> + </p> +<p>Column IDs have the following meanings: <strong>Method ID</strong> -> method ID set for dataset (typically peak calling method ID), <strong># regions</strong> -> number of peak regions used for motif search, <strong># motif hits</strong> -> number of unique motif hits in peak regions (removed double counts), <strong>% regions with motifs</strong> -> percentage of peak regions with motif hits, <strong>% motif nucleotides</strong> -> percentage of unique motif nucleotides over effective peak region size (overlapping regions merged), <strong># motif hits per 1000 nt</strong> -> number of motif hits over 1000 nt of called peak region size (overlapping regions NOT merged).</p> +<h2 id="method-tab-2">k562_eclip,human_v0.1,PUM2 method comparison statistics</h2> +<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> +<table class="sortable"> +<thead> +<tr> +<th style="text-align: center;">Method ID</th> +<th style="text-align: center;"># regions</th> +<th style="text-align: center;"># motif hits</th> +<th style="text-align: center;">% regions with motifs</th> +<th style="text-align: center;">% motif nucleotides</th> +<th style="text-align: center;"># motif hits per 1000 nt</th> +</tr> +</thead> +<tbody> +<tr> +<td style="text-align: center;">dewseq_w100_s5</td> +<td style="text-align: center;">70</td> +<td style="text-align: center;">448</td> +<td style="text-align: center;">92.86</td> +<td style="text-align: center;">14.08</td> +<td style="text-align: center;">31.46</td> +</tr> +<tr> +<td style="text-align: center;">clipper_idr</td> +<td style="text-align: center;">77</td> +<td style="text-align: center;">219</td> +<td style="text-align: center;">76.62</td> +<td style="text-align: center;">17.64</td> +<td style="text-align: center;">46.89</td> +</tr> +</tbody> +</table> +<p> + </p> +<p>Column IDs have the following meanings: <strong>Method ID</strong> -> method ID set for dataset (typically peak calling method ID), <strong># regions</strong> -> number of peak regions used for motif search, <strong># motif hits</strong> -> number of unique motif hits in peak regions (removed double counts), <strong>% regions with motifs</strong> -> percentage of peak regions with motif hits, <strong>% motif nucleotides</strong> -> percentage of unique motif nucleotides over effective peak region size (overlapping regions merged), <strong># motif hits per 1000 nt</strong> -> number of motif hits over 1000 nt of called peak region size (overlapping regions NOT merged).</p> +<h2 id="method-venn-1">k562_eclip,human_v0.1,PUM1 method comparison plot</h2> +<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. +Any given motif hit can either be found only by one method, or be identified by any set (>=2) of methods (intersection areas).</p> +<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 +title="dataset comparison plot k562_eclip,human_v0.1,PUM1" width="700" /></p> +<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> +<p> </p> +<h2 id="method-venn-2">k562_eclip,human_v0.1,PUM2 method comparison plot</h2> +<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. +Any given motif hit can either be found only by one method, or be identified by any set (>=2) of methods (intersection areas).</p> +<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 +title="dataset comparison plot k562_eclip,human_v0.1,PUM2" width="700" /></p> +<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> +<p> </p>