https://wiki.biouml.org/index.php?action=history&feed=atom&title=ROC_curves_for_best_sites_union_%28analysis%29 2026-04-13T06:05:28Z Revision history for this page on the wiki MediaWiki 1.20.3 https://wiki.biouml.org/index.php?title=ROC_curves_for_best_sites_union_(analysis)&diff=6959&oldid=prev 2017-02-13T12:00:18Z

<p>Automatic synchronization with BioUML</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 12:00, 13 February 2017</td> </tr><tr><td colspan="2" class="diff-lineno">Line 13:</td> <td colspan="2" class="diff-lineno">Line 13:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==== Parameters: ====</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==== Parameters: ====</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* '''Input track''' – Select input ChIP-seq track <del class="diffchange diffchange-inline">(must </del>be the result of MACS or SISSRs <del class="diffchange diffchange-inline">analysis</del>)</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* '''Input track''' – Select input <ins class="diffchange diffchange-inline">track (it can be </ins>ChIP-seq track <ins class="diffchange diffchange-inline">from GTRD; thus, it can </ins>be the result of MACS or SISSRs <ins class="diffchange diffchange-inline">peak-finder</ins>)</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Sequences collection''' – Select a source of nucleotide sequences</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Sequences collection''' – Select a source of nucleotide sequences</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>** '''Sequences source''' – Select database to get sequences from or &lt;nowiki&gt;'&lt;/nowiki&gt;Custom&lt;nowiki&gt;'&lt;/nowiki&gt; to specify sequences location manually</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>** '''Sequences source''' – Select database to get sequences from or &lt;nowiki&gt;'&lt;/nowiki&gt;Custom&lt;nowiki&gt;'&lt;/nowiki&gt; to specify sequences location manually</div></td></tr> <tr><td colspan="2" class="diff-lineno">Line 21:</td> <td colspan="2" class="diff-lineno">Line 21:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''% of best sites''' – Best sites percentage</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''% of best sites''' – Best sites percentage</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Types of site models''' – Select site models for comparative analysis</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Types of site models''' – Select site models for comparative analysis</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* '''Matrix''' – Path to <del class="diffchange diffchange-inline">positional weight </del>matrix</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* '''Matrix''' – Path to <ins class="diffchange diffchange-inline">frequency </ins>matrix</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Filtration matrix''' – Path to filtration matrix</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Filtration matrix''' – Path to filtration matrix</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Path to output folder''' – Output folder will be created under this location when it doesn&lt;nowiki&gt;'&lt;/nowiki&gt;t exist</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Path to output folder''' – Output folder will be created under this location when it doesn&lt;nowiki&gt;'&lt;/nowiki&gt;t exist</div></td></tr> </table>

WikiBot https://wiki.biouml.org/index.php?title=ROC_curves_for_best_sites_union_(analysis)&diff=6421&oldid=prev 2015-08-25T05:20:02Z

<p>Automatic synchronization with BioUML</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 05:20, 25 August 2015</td> </tr><tr><td colspan="2" class="diff-lineno">Line 23:</td> <td colspan="2" class="diff-lineno">Line 23:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Matrix''' – Path to positional weight matrix</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Matrix''' – Path to positional weight matrix</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Filtration matrix''' – Path to filtration matrix</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Filtration matrix''' – Path to filtration matrix</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* '''Path to output folder''' – Output folder will be created under this location</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* '''Path to output folder''' – Output folder will be created under this location <ins class="diffchange diffchange-inline">when it doesn&lt;nowiki&gt;'&lt;/nowiki&gt;t exist</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Analyses]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Analyses]]</div></td></tr> </table>

WikiBot https://wiki.biouml.org/index.php?title=ROC_curves_for_best_sites_union_(analysis)&diff=5795&oldid=prev 2014-12-11T09:17:25Z

<p>Automatic synchronization with BioUML</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 09:17, 11 December 2014</td> </tr><tr><td colspan="2" class="diff-lineno">Line 13:</td> <td colspan="2" class="diff-lineno">Line 13:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==== Parameters: ====</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==== Parameters: ====</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* '''Input track''' – Select input <del class="diffchange diffchange-inline">peaks </del>track (must be the result of MACS or SISSRs analysis)</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* '''Input track''' – Select input <ins class="diffchange diffchange-inline">ChIP-seq </ins>track (must be the result of MACS or SISSRs analysis)</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Sequences collection''' – Select a source of nucleotide sequences</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Sequences collection''' – Select a source of nucleotide sequences</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>** '''Sequences source''' – Select database to get sequences from or &lt;nowiki&gt;'&lt;/nowiki&gt;Custom&lt;nowiki&gt;'&lt;/nowiki&gt; to specify sequences location manually</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>** '''Sequences source''' – Select database to get sequences from or &lt;nowiki&gt;'&lt;/nowiki&gt;Custom&lt;nowiki&gt;'&lt;/nowiki&gt; to specify sequences location manually</div></td></tr> </table>

WikiBot https://wiki.biouml.org/index.php?title=ROC_curves_for_best_sites_union_(analysis)&diff=5333&oldid=prev 2013-11-18T07:27:54Z

<p>Automatic synchronization with BioUML</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 07:27, 18 November 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 20:</td> <td colspan="2" class="diff-lineno">Line 20:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Minimal region length''' – Minimal length of sequence region</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Minimal region length''' – Minimal length of sequence region</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''% of best sites''' – Best sites percentage</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''% of best sites''' – Best sites percentage</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">* '''Types of site models''' – Select site models for comparative analysis</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Matrix''' – Path to positional weight matrix</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Matrix''' – Path to positional weight matrix</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Filtration matrix''' – Path to filtration matrix</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Filtration matrix''' – Path to filtration matrix</div></td></tr> </table>

WikiBot https://wiki.biouml.org/index.php?title=ROC_curves_for_best_sites_union_(analysis)&diff=4934&oldid=prev 2013-07-16T11:39:11Z

<p>Automatic synchronization with BioUML</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 11:39, 16 July 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 13:</td> <td colspan="2" class="diff-lineno">Line 13:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==== Parameters: ====</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==== Parameters: ====</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">* '''Input track''' – Select input peaks track (must be the result of MACS or SISSRs analysis)</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Sequences collection''' – Select a source of nucleotide sequences</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Sequences collection''' – Select a source of nucleotide sequences</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>** '''Sequences source''' – Select database to get sequences from or &lt;nowiki&gt;'&lt;/nowiki&gt;Custom&lt;nowiki&gt;'&lt;/nowiki&gt; to specify sequences location manually</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>** '''Sequences source''' – Select database to get sequences from or &lt;nowiki&gt;'&lt;/nowiki&gt;Custom&lt;nowiki&gt;'&lt;/nowiki&gt; to specify sequences location manually</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>** '''Sequence collection''' – Specify path to folder containing sequences if &lt;nowiki&gt;'&lt;/nowiki&gt;Custom&lt;nowiki&gt;'&lt;/nowiki&gt; sequences source is selected</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>** '''Sequence collection''' – Specify path to folder containing sequences if &lt;nowiki&gt;'&lt;/nowiki&gt;Custom&lt;nowiki&gt;'&lt;/nowiki&gt; sequences source is selected</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">* '''Input track''' – Select input peaks track (must be the result of MACS or SISSRs analysis)</del></div></td><td colspan="2">&#160;</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Is around summit''' – Is around summit</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Is around summit''' – Is around summit</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Minimal region length''' – Minimal length of sequence region</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Minimal region length''' – Minimal length of sequence region</div></td></tr> </table>

WikiBot https://wiki.biouml.org/index.php?title=ROC_curves_for_best_sites_union_(analysis)&diff=4910&oldid=prev 2013-07-09T11:12:31Z

<p>Protected &quot;<a href="/index.php/ROC_curves_for_best_sites_union_(analysis)" title="ROC curves for best sites union (analysis)">ROC curves for best sites union (analysis)</a>&quot;: Autogenerated page (‎[edit=sysop] (indefinite))</p> <table class='diff diff-contentalign-left'> <tr style='vertical-align: top;'> <td colspan='1' style="background-color: white; color:black;">← Older revision</td> <td colspan='1' style="background-color: white; color:black;">Revision as of 11:12, 9 July 2013</td> </tr></table>

WikiBot https://wiki.biouml.org/index.php?title=ROC_curves_for_best_sites_union_(analysis)&diff=4909&oldid=prev 2013-07-09T11:12:30Z

<p>Automatic synchronization with BioUML</p> <p><b>New page</b></p><div>;Analysis title<br /> :[[File:Default-analysis-icon.png]] ROC curves for best sites union<br /> ;Provider<br /> :[[Institute of Systems Biology]]<br /> ;Class<br /> :{{Class|biouml.plugins.bindingregions.fiveSiteModels.BestSitesUnionROCCurves}}<br /> ;Plugin<br /> :[[Biouml.plugins.bindingregions (plugin)|biouml.plugins.bindingregions (Binding-regions related analyses)]]<br /> <br /> ==== Description ====<br /> Best sites: ROC-curves; union of best sites in single chip-seq track; summit(yes/no); filtration (yes/no); matrix derivation.<br /> <br /> ==== Parameters: ====<br /> <br /> * '''Sequences collection''' – Select a source of nucleotide sequences<br /> ** '''Sequences source''' – Select database to get sequences from or &lt;nowiki&gt;'&lt;/nowiki&gt;Custom&lt;nowiki&gt;'&lt;/nowiki&gt; to specify sequences location manually<br /> ** '''Sequence collection''' – Specify path to folder containing sequences if &lt;nowiki&gt;'&lt;/nowiki&gt;Custom&lt;nowiki&gt;'&lt;/nowiki&gt; sequences source is selected<br /> * '''Input track''' – Select input peaks track (must be the result of MACS or SISSRs analysis)<br /> * '''Is around summit''' – Is around summit<br /> * '''Minimal region length''' – Minimal length of sequence region<br /> * '''% of best sites''' – Best sites percentage<br /> * '''Matrix''' – Path to positional weight matrix<br /> * '''Filtration matrix''' – Path to filtration matrix<br /> * '''Path to output folder''' – Output folder will be created under this location<br /> <br /> [[Category:Analyses]]<br /> [[Category:Binding regions (analyses group)]]<br /> [[Category:ISB analyses]]<br /> [[Category:Autogenerated pages]]</div>

WikiBot