https://wiki.biouml.org/index.php?action=history&feed=atom&title=Calculate_keynodes_ranks_%28analysis%29 2026-04-21T02:25:20Z Revision history for this page on the wiki MediaWiki 1.20.3 https://wiki.biouml.org/index.php?title=Calculate_keynodes_ranks_(analysis)&diff=8866&oldid=prev 2020-12-09T11:15:01Z

<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 11:15, 9 December 2020</td> </tr><tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Analysis title</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Analysis title</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:[[File:<del class="diffchange diffchange-inline">Default</del>-<del class="diffchange diffchange-inline">analysis</del>-icon.png]] Calculate keynodes ranks</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:[[File:<ins class="diffchange diffchange-inline">Genome</ins>-<ins class="diffchange diffchange-inline">enhancer-Calculate-keynodes-ranks</ins>-icon.png]] Calculate keynodes ranks</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Provider</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Provider</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:[[Biosoft]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:[[Biosoft]]</div></td></tr> <tr><td colspan="2" class="diff-lineno">Line 9:</td> <td colspan="2" class="diff-lineno">Line 9:</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>==== Description ====</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==== Description ====</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">Calculates keynodes ranks using proteome</del>, <del class="diffchange diffchange-inline">transcriptome </del>and CMA</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">This method takes the result of keynode analysis with additional column of gene identifiers. It adds optional score columns from three other tables called ''Transcriptome''</ins>, <ins class="diffchange diffchange-inline">''Proteome'' </ins>and <ins class="diffchange diffchange-inline">''</ins>CMA <ins class="diffchange diffchange-inline">score table''. Any table of gene identifiers with numerical score column can be set as any of these three tables.</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>&#160;</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 class="diffchange diffchange-inline">The result is ranked via the Keynodes Score column and via the newly added scores. The ranking procedure used is the following: molecules are sorted in descending order of scores and then integer numbers starting from 1 are assigned to each molecule. Molecules with the same score obtain the same rank number. The Total Rank is the sum of score-specific ranks for each molecule.</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>==== 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 colspan="2" class="diff-lineno">Line 16:</td> <td colspan="2" class="diff-lineno">Line 18:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Column with gene IDs''' – Column with gene IDs</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Column with gene IDs''' – Column with gene IDs</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Transcriptome''' – Path to transcriptome data table</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Transcriptome''' – Path to transcriptome data table</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;">* '''Optional transcriptome''' – Use transcriptomics score if present and skip if not present</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Score column (transcriptome)''' – Score column (transcriptome)</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Score column (transcriptome)''' – Score column (transcriptome)</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Proteome''' – Path to proteome data table</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Proteome''' – Path to proteome data table</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Score column (proteome)''' – Score column (proteome)</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Score column (proteome)''' – Score column (proteome)</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* '''CMA <del class="diffchange diffchange-inline">result</del>''' – Path to CMA result</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* '''CMA <ins class="diffchange diffchange-inline">score table</ins>''' – Path to <ins class="diffchange diffchange-inline">table with CMA model scores calculated (e.g. Model visualization table from </ins>CMA result<ins class="diffchange diffchange-inline">)</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Result''' – Path to result table</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Result''' – Path to result table</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> </table>

WikiBot https://wiki.biouml.org/index.php?title=Calculate_keynodes_ranks_(analysis)&diff=7777&oldid=prev 2019-03-12T09:33:29Z

<p>Protected &quot;<a href="/index.php/Calculate_keynodes_ranks_(analysis)" title="Calculate keynodes ranks (analysis)">Calculate keynodes ranks (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 09:33, 12 March 2019</td> </tr></table>

WikiBot https://wiki.biouml.org/index.php?title=Calculate_keynodes_ranks_(analysis)&diff=7773&oldid=prev 2019-03-12T09:33:26Z

<p>Automatic synchronization with BioUML</p> <p><b>New page</b></p><div>;Analysis title<br /> :[[File:Default-analysis-icon.png]] Calculate keynodes ranks<br /> ;Provider<br /> :[[Biosoft]]<br /> ;Class<br /> :{{Class|biouml.plugins.genomeenhancer.analysis.GEKnRankCalculator}}<br /> ;Plugin<br /> :[[Biouml.plugins.genomeenhancer (plugin)|biouml.plugins.genomeenhancer (Genome Enhancer)]]<br /> <br /> ==== Description ====<br /> Calculates keynodes ranks using proteome, transcriptome and CMA<br /> <br /> ==== Parameters: ====<br /> <br /> * '''Keynodes result''' – Path to table with keynodes result<br /> * '''Column with gene IDs''' – Column with gene IDs<br /> * '''Transcriptome''' – Path to transcriptome data table<br /> * '''Score column (transcriptome)''' – Score column (transcriptome)<br /> * '''Proteome''' – Path to proteome data table<br /> * '''Score column (proteome)''' – Score column (proteome)<br /> * '''CMA result''' – Path to CMA result<br /> * '''Result''' – Path to result table<br /> <br /> [[Category:Analyses]]<br /> [[Category:Genome enhancer (analyses group)]]<br /> [[Category:Biosoft analyses]]<br /> [[Category:Autogenerated pages]]</div>

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