Difference between revisions of "Biouml.plugins.bindingregions (plugin)"
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:[[Institute of Systems Biology]] | :[[Institute of Systems Biology]] | ||
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=== Extension points === | === Extension points === | ||
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*[[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]] [[Common and IPS scores correlation (analysis)|Common and IPS scores correlation]] | *[[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]] [[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]] [[Create matrix by mixture of normal components (ChIP-seq) (analysis)|Create matrix by mixture of normal components (ChIP-seq)]] | *[[File:Default-analysis-icon.png]] [[Create matrix by mixture of normal components (ChIP-seq) (analysis)|Create matrix by mixture of normal components (ChIP-seq)]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Discrimination between high and low translation efficiencies (analysis)|Discrimination between high and low translation efficiencies]] | ||
*[[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]] [[Filtration of predicted sites by filters (analysis)|Filtration of predicted sites by filters]] | ||
*[[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]] [[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]] [[Locations of best sites (analysis)|Locations of best sites]] | *[[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]] [[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]] [[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 mRNA fragments (analysis)|Oligonucleotides in mRNA fragments]] | ||
*[[File:Default-analysis-icon.png]] [[Peak finders comparison (analysis)|Peak finders comparison]] | *[[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 for best sites union (analysis)|ROC curves for best sites union]] | ||
| − | *[[File:Default-analysis-icon.png]] [[ROC curves in grouped peaks (analysis)|ROC curves in grouped peaks]] | + | *[[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]] [[Ribo-Seq and mRNA features (analysis)|Ribo-Seq and mRNA features]] | ||
*[[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]] [[Start codon clusterization (analysis)|Start codon clusterization]] | ||
*[[File:Default-analysis-icon.png]] [[Summary on AUCs (analysis)|Summary on AUCs]] | *[[File:Default-analysis-icon.png]] [[Summary on AUCs (analysis)|Summary on AUCs]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Two multivariate sample 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]] | ||
Revision as of 16:19, 11 December 2014
- ID
- biouml.plugins.bindingregions
- Name
- Binding-regions related analyses
- Provider
- Institute of Systems Biology
- Version
- 0.9.8
Extension points
Extension points defined in this plugin:
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
- Common and IPS scores correlation
- Convert files to tracks
- Correlations of best sites
- Count olig frequencies
- Create matrix by mixture of normal components
- Create matrix by mixture of normal components (ChIP-seq)
- Discrimination between high and low translation efficiencies
- Distinct TF classes
- Filtration of predicted sites by filters
- 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
- Locations of best sites
- Matrix comparison
- Merge binding regions for cell-lines
- Mixture of normal components
- Non-merged ChIP-Seq tracks summary
- Oligonucleotides in mRNA fragments
- 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
- Ribo-Seq and mRNA features
- SNP regions in genome
- SNPs in binding regions
- Start codon clusterization
- Summary on AUCs
- Two multivariate sample analysis
- lincRNA and mRNA features
