Mixture of normal components (analysis) - Revision history

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2013-06-17T06:38:44Z

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WikiBot: Protected "Mixture of normal components (analysis)": Autogenerated page (‎[edit=sysop] (indefinite))

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2013-06-07T10:39:53Z

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;Analysis title
:[[File:Binding-regions-Mixture-of-normal-components-icon.png]] Mixture of normal components
;Provider
:[[Institute of Systems Biology]]
;Class
:{{Class|ru.biosoft.bsa.analysis.bindingRegions.NormalComponentsMixture}}
;Plugin
:[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]]

==== Description ====
Mixture of normal components for maximal IPS scores predicted in binding regions (singleTrack) of given tfClass (charts table is created)

==== Parameters: ====

* '''Input track''' – Select input ChIP-seq track (must be the result of <nowiki>'</nowiki>Merge binding regions for cell-lines<nowiki>'</nowiki> analysis)
* '''Matrix''' – Path to positional weight matrix
* '''TF class''' – TF class in Wingender classification (like <nowiki>'</nowiki>1.1.2.1<nowiki>'</nowiki>)
* '''Number of mixture components''' – Number of mixture components
* '''P-value''' – P-value
* '''Output table''' – Table with charts will be created in this location

[[Category:Analyses]]
[[Category:Binding regions (analyses group)]]
[[Category:ISB analyses]]
[[Category:Autogenerated pages]]

@@ Line 20: / Line 20: @@
 * '''Minimal region length''' – Minimal length of sequence region
 * '''Input track''' – Select input track (it must contain ChIP-Seq peaks or merged binding regions depending on input parameter <nowiki>'</nowiki>Is ChIP-Seq peaks<nowiki>'</nowiki>
-* '''Matrix''' – Path to positional weight matrix
+* '''Matrix''' – Path to frequency matrix
-* '''Type of site model''' – Type of site model
+* '''Type of site model''' – Select type of site model
-* '''Number of mixture components''' – Number of mixture components
+* '''Number of mixture components''' – Define number of mixture components (it must be > 1
 * '''P-value threshold''' – P-value threshold
-* '''Max iterations''' – Maximal number of iterations for algorithm
+* '''Maximal number of iterations''' – Maximal number of iterations in algorithm
 * '''Output table''' – Table with charts will be created in this location

@@ Line 23: / Line 23: @@
 * '''Type of site model''' – Type of site model
 * '''Number of mixture components''' – Number of mixture components
-* '''P-value''' – P-value
+* '''P-value threshold''' – P-value threshold
 * '''Max iterations''' – Maximal number of iterations for algorithm
 * '''Output table''' – Table with charts will be created in this location

@@ Line 13: / Line 13: @@
 ==== Parameters: ====
-* '''Input track''' – Select input ChIP-seq track (must be the result of <nowiki>'</nowiki>Merge binding regions for cell-lines<nowiki>'</nowiki> analysis)
+* '''Sequences collection''' – Select a source of nucleotide sequences
-* '''Matrix''' – Path to positional weight matrix
+** '''Sequences source''' – Select database to get sequences from or <nowiki>'</nowiki>Custom<nowiki>'</nowiki> to specify sequences location manually
 * '''TF class''' – TF class in Wingender classification (like <nowiki>'</nowiki>2.1.1.1.4<nowiki>'</nowiki>)
 * '''Number of mixture components''' – Number of mixture components
 * '''P-value''' – P-value
 * '''Output table''' – Table with charts will be created in this location

@@ Line 4: / Line 4: @@
 :[[Institute of Systems Biology]]
 ;Class
-:{{Class|ru.biosoft.bsa.analysis.bindingRegions.NormalComponentsMixture}}
+:{{Class|biouml.plugins.bindingregions.analysis.NormalComponentsMixture}}
 ;Plugin
-:[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]]
+:[[Biouml.plugins.bindingregions (plugin)|biouml.plugins.bindingregions (Binding-regions related analyses)]]
 ==== Description ====

@@ Line 1: / Line 1: @@
 ;Analysis title
-:[[File:Binding-regions-Mixture-of-normal-components-icon.png]] Mixture of normal components
+:[[File:Default-analysis-icon.png]] Mixture of normal components
 ;Provider
 :[[Institute of Systems Biology]]