Difference between revisions of "Mixture of normal components (analysis)"
From BioUML platform
m (Protected "Mixture of normal components (analysis)": Autogenerated page ([edit=sysop] (indefinite))) |
(Automatic synchronization with BioUML) |
||
| (5 intermediate revisions by one user not shown) | |||
| Line 1: | Line 1: | ||
;Analysis title | ;Analysis title | ||
| − | :[[File: | + | :[[File:Default-analysis-icon.png]] Mixture of normal components |
;Provider | ;Provider | ||
:[[Institute of Systems Biology]] | :[[Institute of Systems Biology]] | ||
;Class | ;Class | ||
| − | :{{Class| | + | :{{Class|biouml.plugins.bindingregions.analysis.NormalComponentsMixture}} |
;Plugin | ;Plugin | ||
| − | :[[ | + | :[[Biouml.plugins.bindingregions (plugin)|biouml.plugins.bindingregions (Binding-regions related analyses)]] |
==== Description ==== | ==== Description ==== | ||
| Line 13: | Line 13: | ||
==== Parameters: ==== | ==== Parameters: ==== | ||
| − | * ''' | + | * '''Sequences collection''' – Select a source of nucleotide sequences |
| − | * ''' | + | ** '''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>1.1. | + | ** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> sequences source is selected |
| − | * '''Number of mixture components''' – | + | * '''Is ChIP-Seq peaks''' – Is ChIP-Seq peaks (or merged binding regions) |
| − | * '''P-value''' – P-value | + | * '''TF class''' – TF class in Wingender classification (like <nowiki>'</nowiki>2.1.1.1.4<nowiki>'</nowiki>) |
| + | * '''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 frequency matrix | ||
| + | * '''Type of site model''' – Select type of site model | ||
| + | * '''Number of mixture components''' – Define number of mixture components (it must be > 1 | ||
| + | * '''P-value threshold''' – P-value threshold | ||
| + | * '''Maximal number of iterations''' – Maximal number of iterations in algorithm | ||
* '''Output table''' – Table with charts will be created in this location | * '''Output table''' – Table with charts will be created in this location | ||
Latest revision as of 19:00, 13 February 2017
- Analysis title
Mixture of normal components
- Provider
- Institute of Systems Biology
- Class
NormalComponentsMixture- Plugin
- biouml.plugins.bindingregions (Binding-regions related analyses)
[edit] Description
Mixture of normal components for maximal IPS scores predicted in binding regions (singleTrack) of given tfClass (charts table is created)
[edit] Parameters:
- Sequences collection – Select a source of nucleotide sequences
- Sequences source – Select database to get sequences from or 'Custom' to specify sequences location manually
- Sequence collection – Specify path to folder containing sequences if 'Custom' sequences source is selected
- Is ChIP-Seq peaks – Is ChIP-Seq peaks (or merged binding regions)
- TF class – TF class in Wingender classification (like '2.1.1.1.4')
- 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 'Is ChIP-Seq peaks'
- Matrix – Path to frequency matrix
- Type of site model – Select type of site model
- Number of mixture components – Define number of mixture components (it must be > 1
- P-value threshold – P-value threshold
- Maximal number of iterations – Maximal number of iterations in algorithm
- Output table – Table with charts will be created in this location
