Difference between revisions of "Mixture of normal components (analysis)"
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==== 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 |
| + | ** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> sequences source is selected | ||
| + | * '''Is ChIP-Seq peaks''' – Is ChIP-Seq peaks (or merged binding regions) | ||
* '''TF class''' – TF class in Wingender classification (like <nowiki>'</nowiki>2.1.1.1.4<nowiki>'</nowiki>) | * '''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 positional weight matrix | ||
| + | * '''Type of site model''' – Type of site model | ||
* '''Number of mixture components''' – Number of mixture components | * '''Number of mixture components''' – Number of mixture components | ||
* '''P-value''' – P-value | * '''P-value''' – P-value | ||
| + | * '''Max iterations''' – Maximal number of iterations for algorithm | ||
* '''Output table''' – Table with charts will be created in this location | * '''Output table''' – Table with charts will be created in this location | ||
Revision as of 16:17, 11 December 2014
- Analysis title
Mixture of normal components
- Provider
- Institute of Systems Biology
- Class
NormalComponentsMixture- Plugin
- biouml.plugins.bindingregions (Binding-regions related analyses)
Description
Mixture of normal components for maximal IPS scores predicted in binding regions (singleTrack) of given tfClass (charts table is created)
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 positional weight matrix
- Type of site model – Type of site model
- Number of mixture components – Number of mixture components
- P-value – P-value
- Max iterations – Maximal number of iterations for algorithm
- Output table – Table with charts will be created in this location
