Difference between revisions of "Biouml.plugins.bindingregions (plugin)"
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:[[Institute of Systems Biology]] | :[[Institute of Systems Biology]] | ||
;Version | ;Version | ||
| − | :0.9. | + | :0.9.10 |
| + | |||
| + | === Extension points === | ||
| + | Extension points defined in this plugin: | ||
| + | *[[Site model factory (extension point)|biouml.plugins.bindingregions.siteModelFactory]] | ||
=== Analysis methods === | === Analysis methods === | ||
Analysis methods defined in this plugin: | Analysis methods defined in this plugin: | ||
| + | *[[File:Default-analysis-icon.png]] [[Analysis of Binding Regions (analysis)|Analysis of Binding Regions]] | ||
*[[File:Default-analysis-icon.png]] [[Analysis of Cis-Regulatory Modules (analysis)|Analysis of Cis-Regulatory Modules]] | *[[File:Default-analysis-icon.png]] [[Analysis of Cis-Regulatory Modules (analysis)|Analysis of Cis-Regulatory Modules]] | ||
| − | |||
*[[File:Default-analysis-icon.png]] [[Binding regions summary (analysis)|Binding regions summary]] | *[[File:Default-analysis-icon.png]] [[Binding regions summary (analysis)|Binding regions summary]] | ||
| + | *[[File:Default-analysis-icon.png]] [[CRISPR Cas9 and specific oligonucleotides (analysis)|CRISPR Cas9 and specific oligonucleotides]] | ||
*[[File:Default-analysis-icon.png]] [[ChIP-Seq characteristics distribution (analysis)|ChIP-Seq characteristics distribution]] | *[[File:Default-analysis-icon.png]] [[ChIP-Seq characteristics distribution (analysis)|ChIP-Seq characteristics distribution]] | ||
| + | *[[File:Default-analysis-icon.png]] [[ChIP-Seq peaks clusterization (analysis)|ChIP-Seq peaks clusterization]] | ||
*[[File:Default-analysis-icon.png]] [[Cis-module identification (analysis)|Cis-module identification]] | *[[File:Default-analysis-icon.png]] [[Cis-module identification (analysis)|Cis-module identification]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Cis-module sets near given genes (analysis)|Cis-module sets near given genes]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Classification analysis]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Cluster analysis]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Common and IPS scores correlation (analysis)|Common and IPS scores correlation]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Convert files to tracks (analysis)|Convert files to tracks]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Correlations of best sites (analysis)|Correlations of best sites]] | ||
*[[File:Default-analysis-icon.png]] [[Count olig frequencies (analysis)|Count olig frequencies]] | *[[File:Default-analysis-icon.png]] [[Count olig frequencies (analysis)|Count olig frequencies]] | ||
*[[File:Default-analysis-icon.png]] [[Create matrix by mixture of normal components (analysis)|Create matrix by mixture of normal components]] | *[[File:Default-analysis-icon.png]] [[Create matrix by mixture of normal components (analysis)|Create matrix by mixture of normal components]] | ||
| − | *[[File:Default-analysis-icon.png]] [[ | + | *[[File:Default-analysis-icon.png]] [[Data matrix operations (analysis)|Data matrix operations]] |
*[[File:Default-analysis-icon.png]] [[Distinct TF classes (analysis)|Distinct TF classes]] | *[[File:Default-analysis-icon.png]] [[Distinct TF classes (analysis)|Distinct TF classes]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Fantom analysis]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Filtration of predicted sites by filters (analysis)|Filtration of predicted sites by filters]] | ||
| + | *[[File:Default-analysis-icon.png]] [[GTRD analysis]] | ||
| + | *[[File:Default-analysis-icon.png]] [[GTRD analysis advanced (analysis)|GTRD analysis advanced]] | ||
*[[File:Default-analysis-icon.png]] [[Gathering genome statistics (analysis)|Gathering genome statistics]] | *[[File:Default-analysis-icon.png]] [[Gathering genome statistics (analysis)|Gathering genome statistics]] | ||
*[[File:Default-analysis-icon.png]] [[IPS ROC-curves (analysis)|IPS ROC-curves]] | *[[File:Default-analysis-icon.png]] [[IPS ROC-curves (analysis)|IPS ROC-curves]] | ||
*[[File:Default-analysis-icon.png]] [[IPS prediction (analysis)|IPS prediction]] | *[[File:Default-analysis-icon.png]] [[IPS prediction (analysis)|IPS prediction]] | ||
*[[File:Default-analysis-icon.png]] [[IPS-scores in SNPs (analysis)|IPS-scores in SNPs]] | *[[File:Default-analysis-icon.png]] [[IPS-scores in SNPs (analysis)|IPS-scores in SNPs]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Identical best site ROC-curves (analysis)|Identical best site ROC-curves]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Identification of cis-regulatory modules with given pattern of TF-classes (analysis)|Identification of cis-regulatory modules with given pattern of TF-classes]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Identification of composite elements by filters (analysis)|Identification of composite elements by filters]] | ||
| + | *[[File:Default-analysis-icon.png]] [[LS-regression analysis]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Locations of best sites (analysis)|Locations of best sites]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Matrix comparison (analysis)|Matrix comparison]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Matrix derivation (analysis)|Matrix derivation]] | ||
*[[File:Default-analysis-icon.png]] [[Merge binding regions for cell-lines (analysis)|Merge binding regions for cell-lines]] | *[[File:Default-analysis-icon.png]] [[Merge binding regions for cell-lines (analysis)|Merge binding regions for cell-lines]] | ||
*[[File:Default-analysis-icon.png]] [[Mixture of normal components (analysis)|Mixture of normal components]] | *[[File:Default-analysis-icon.png]] [[Mixture of normal components (analysis)|Mixture of normal components]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Multivariate regression analysis]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Multivariate sample analysis]] | ||
*[[File:Default-analysis-icon.png]] [[Non-merged ChIP-Seq tracks summary (analysis)|Non-merged ChIP-Seq tracks summary]] | *[[File:Default-analysis-icon.png]] [[Non-merged ChIP-Seq tracks summary (analysis)|Non-merged ChIP-Seq tracks summary]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Oligonucleotides in sequence samples (analysis)|Oligonucleotides in sequence samples]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Peak finders comparison (analysis)|Peak finders comparison]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Prediction of TF-binding sites of given TF (analysis)|Prediction of TF-binding sites of given TF]] | ||
| + | *[[File:Default-analysis-icon.png]] [[ROC curves for best sites union (analysis)|ROC curves for best sites union]] | ||
| + | *[[File:Default-analysis-icon.png]] [[ROC-curves in clusterized peaks (analysis)|ROC-curves in clusterized peaks]] | ||
| + | *[[File:Default-analysis-icon.png]] [[ROC-curves in grouped peaks (analysis)|ROC-curves in grouped peaks]] | ||
| + | *[[File:Default-analysis-icon.png]] [[ROC-curves in overlapped ChIP-Seq peaks (analysis)|ROC-curves in overlapped ChIP-Seq peaks]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Regression analysis]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Ribo-Seq and mRNA features forming (analysis)|Ribo-Seq and mRNA features forming]] | ||
*[[File:Default-analysis-icon.png]] [[SNP regions in genome (analysis)|SNP regions in genome]] | *[[File:Default-analysis-icon.png]] [[SNP regions in genome (analysis)|SNP regions in genome]] | ||
*[[File:Default-analysis-icon.png]] [[SNPs in binding regions (analysis)|SNPs in binding regions]] | *[[File:Default-analysis-icon.png]] [[SNPs in binding regions (analysis)|SNPs in binding regions]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Summary on AUCs (analysis)|Summary on AUCs]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Transform track to table (analysis)|Transform track to table]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Two multivariate sample analysis]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Univariate sample analysis]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Univariate samples analysis]] | ||
| + | *[[File:Default-analysis-icon.png]] [[LincRNA and mRNA features (analysis)|lincRNA and mRNA features]] | ||
[[Category:Plugins]] | [[Category:Plugins]] | ||
[[Category:ISB plugins]] | [[Category:ISB plugins]] | ||
[[Category:Autogenerated pages]] | [[Category:Autogenerated pages]] | ||
Latest revision as of 16:35, 12 March 2019
- ID
- biouml.plugins.bindingregions
- Name
- Binding-regions related analyses
- Provider
- Institute of Systems Biology
- Version
- 0.9.10
[edit] Extension points
Extension points defined in this plugin:
[edit] Analysis methods
Analysis methods defined in this plugin:
Analysis of Binding Regions
- Analysis of Cis-Regulatory Modules
- Binding regions summary
- CRISPR Cas9 and specific oligonucleotides
- ChIP-Seq characteristics distribution
- ChIP-Seq peaks clusterization
- Cis-module identification
- Cis-module sets near given genes
- Classification analysis
- Cluster analysis
- Common and IPS scores correlation
- Convert files to tracks
- Correlations of best sites
- Count olig frequencies
- Create matrix by mixture of normal components
- Data matrix operations
- Distinct TF classes
- Fantom analysis
- Filtration of predicted sites by filters
- GTRD analysis
- GTRD analysis advanced
- Gathering genome statistics
- IPS ROC-curves
- IPS prediction
- IPS-scores in SNPs
- Identical best site ROC-curves
- Identification of cis-regulatory modules with given pattern of TF-classes
- Identification of composite elements by filters
- LS-regression analysis
- Locations of best sites
- Matrix comparison
- Matrix derivation
- Merge binding regions for cell-lines
- Mixture of normal components
- Multivariate regression analysis
- Multivariate sample analysis
- Non-merged ChIP-Seq tracks summary
- Oligonucleotides in sequence samples
- Peak finders comparison
- Prediction of TF-binding sites of given TF
- ROC curves for best sites union
- ROC-curves in clusterized peaks
- ROC-curves in grouped peaks
- ROC-curves in overlapped ChIP-Seq peaks
- Regression analysis
- Ribo-Seq and mRNA features forming
- SNP regions in genome
- SNPs in binding regions
- Summary on AUCs
- Transform track to table
- Two multivariate sample analysis
- Univariate sample analysis
- Univariate samples analysis
- lincRNA and mRNA features
