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Common and IPS scores correlation (analysis) - Revision history
2026-04-12T20:56:01Z
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WikiBot: Automatic synchronization with BioUML
2017-02-13T12:00:07Z
<p>Automatic synchronization with BioUML</p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** '''Sequences source''' – Select database to get sequences from or <nowiki>'</nowiki>Custom<nowiki>'</nowiki> to specify sequences location manually</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** '''Sequences source''' – Select database to get sequences from or <nowiki>'</nowiki>Custom<nowiki>'</nowiki> to specify sequences location manually</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> sequences source is selected</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> sequences source is selected</div></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'> </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'> </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'>−</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'> </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<nowiki>'</nowiki>t exist</div></td><td class='diff-marker'> </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<nowiki>'</nowiki>t exist</div></td></tr>
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WikiBot: Automatic synchronization with BioUML
2015-08-25T05:19:53Z
<p>Automatic synchronization with BioUML</p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 05:19, 25 August 2015</td>
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<tr><td class='diff-marker'> </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'> </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'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Matrix''' – Path to positional weight matrix</div></td><td class='diff-marker'> </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'>−</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<nowiki>'</nowiki>t exist</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Analyses]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Analyses]]</div></td></tr>
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WikiBot: Automatic synchronization with BioUML
2014-12-11T09:17:17Z
<p>Automatic synchronization with BioUML</p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 09:17, 11 December 2014</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** '''Sequences source''' – Select database to get sequences from or <nowiki>'</nowiki>Custom<nowiki>'</nowiki> to specify sequences location manually</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** '''Sequences source''' – Select database to get sequences from or <nowiki>'</nowiki>Custom<nowiki>'</nowiki> to specify sequences location manually</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> sequences source is selected</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> sequences source is selected</div></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 (must be the result of <del class="diffchange diffchange-inline"><nowiki>'</nowiki>Merge binding regions for cell-lines<nowiki>'</nowiki> </del>analysis)</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* '''Input track''' – Select input ChIP-seq track (must be the result of <ins class="diffchange diffchange-inline">MACS or SISSRs </ins>analysis)</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">* '''Matrix''' – Path to positional weight matrix</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'> </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'> </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'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* '''<del class="diffchange diffchange-inline">Output table</del>''' – <del class="diffchange diffchange-inline">Table with charts </del>will be created <del class="diffchange diffchange-inline">in </del>this location</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* '''<ins class="diffchange diffchange-inline">Matrix</ins>''' – <ins class="diffchange diffchange-inline">Path to positional weight matrix</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* '''Path to output folder''' – Output folder </ins>will be created <ins class="diffchange diffchange-inline">under </ins>this location</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Analyses]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Analyses]]</div></td></tr>
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WikiBot: Protected "Common and IPS scores correlation (analysis)": Autogenerated page ([edit=sysop] (indefinite))
2013-06-27T05:59:47Z
<p>Protected "<a href="/index.php/Common_and_IPS_scores_correlation_(analysis)" title="Common and IPS scores correlation (analysis)">Common and IPS scores correlation (analysis)</a>": Autogenerated page ([edit=sysop] (indefinite))</p>
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<td colspan='1' style="background-color: white; color:black;">Revision as of 05:59, 27 June 2013</td>
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WikiBot: Automatic synchronization with BioUML
2013-06-27T05:59:46Z
<p>Automatic synchronization with BioUML</p>
<p><b>New page</b></p><div>;Analysis title<br />
:[[File:Default-analysis-icon.png]] Common and IPS scores correlation<br />
;Provider<br />
:[[Institute of Systems Biology]]<br />
;Class<br />
:{{Class|biouml.plugins.bindingregions.analysis.CommonAndIPSCorrelation}}<br />
;Plugin<br />
:[[Biouml.plugins.bindingregions (plugin)|biouml.plugins.bindingregions (Binding-regions related analyses)]]<br />
<br />
==== Description ====<br />
Correlation between common score and IPS-score for best IPS-sites in single Chip-Seq track<br />
<br />
==== Parameters: ====<br />
<br />
* '''Sequences collection''' – Select a source of nucleotide sequences<br />
** '''Sequences source''' – Select database to get sequences from or <nowiki>'</nowiki>Custom<nowiki>'</nowiki> to specify sequences location manually<br />
** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> sequences source is selected<br />
* '''Input track''' – Select input ChIP-seq track (must be the result of <nowiki>'</nowiki>Merge binding regions for cell-lines<nowiki>'</nowiki> analysis)<br />
* '''Matrix''' – Path to positional weight matrix<br />
* '''Minimal region length''' – Minimal length of sequence region<br />
* '''Output table''' – Table with charts will be created in this location<br />
<br />
[[Category:Analyses]]<br />
[[Category:Binding regions (analyses group)]]<br />
[[Category:ISB analyses]]<br />
[[Category:Autogenerated pages]]</div>
WikiBot