https://help.rc.ufl.edu/mediawiki/index.php?title=LEfSe&feed=atom&action=history
LEfSe - Revision history
2024-03-28T23:50:06Z
Revision history for this page on the wiki
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https://help.rc.ufl.edu/mediawiki/index.php?title=LEfSe&diff=20622&oldid=prev
Maxprok: Created page with "Category:SoftwareCategory:Phylogenetics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|lefse}} |{{#vardefine:url|https://bioconda.github.io/recipes/lefse/README.ht..."
2020-09-29T20:14:38Z
<p>Created page with "<a href="/doc/Category:Software" title="Category:Software">Category:Software</a><a href="/doc/Category:Phylogenetics" title="Category:Phylogenetics">Category:Phylogenetics</a> {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|lefse}} |{{#vardefine:url|https://bioconda.github.io/recipes/lefse/README.ht..."</p>
<p><b>New page</b></p><div>[[Category:Software]][[Category:Phylogenetics]]<br />
{|<!--CONFIGURATION: REQUIRED--><br />
|{{#vardefine:app|lefse}}<br />
|{{#vardefine:url|https://bioconda.github.io/recipes/lefse/README.html}}<br />
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--><br />
|{{#vardefine:conf|}} <!--CONFIGURATION--><br />
|{{#vardefine:exe|}} <!--ADDITIONAL INFO--><br />
|{{#vardefine:job|}} <!--JOB SCRIPTS--><br />
|{{#vardefine:policy|}} <!--POLICY--><br />
|{{#vardefine:testing|}} <!--PROFILING--><br />
|{{#vardefine:faq|}} <!--FAQ--><br />
|{{#vardefine:citation|}} <!--CITATION--><br />
|{{#vardefine:installation|}} <!--INSTALLATION--><br />
|}<br />
<!--BODY--><br />
<!--Description--><br />
{{#if: {{#var: url}}|<br />
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}<br />
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LDA Effect Size (LEfSe) (Segata et. al 2010) is an algorithm for high-dimensional biomarker discovery and explanation that identifies genomic features (genes, pathways, or taxa) characterizing the differences between two or more biological conditions.<br />
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==Environment Modules==<br />
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.<br />
==System Variables==<br />
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory<br />
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory<br />
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{{#if: {{#var: conf}}|==Configuration==<br />
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.<br />
|}}<br />
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{{#if: {{#var: exe}}|==Additional Information==<br />
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WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY<br />
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|}}<br />
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{{#if: {{#var: job}}|==Job Script Examples==<br />
See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} Job script examples.<br />
|}}<br />
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{{#if: {{#var: policy}}|==Usage Policy==<br />
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WRITE USAGE POLICY HERE (Licensing, usage, access).<br />
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|}}<br />
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{{#if: {{#var: testing}}|==Performance==<br />
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WRITE_PERFORMANCE_TESTING_RESULTS_HERE<br />
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|}}<br />
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{{#if: {{#var: faq}}|==FAQ==<br />
*'''Q:''' **'''A:'''|}}<br />
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{{#if: {{#var: citation}}|==Citation==<br />
If you publish research that uses {{#var:app}} you have to cite it as follows:<br />
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WRITE_CITATION_HERE<br />
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|}}<br />
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{{#if: {{#var: installation}}|==Installation==<br />
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}<br />
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__NOTOC____NOEDITSECTION__</div>
Maxprok