Difference between revisions of "Biouml.plugins.bindingregions (plugin)"
From BioUML platform
(Automatic synchronization with BioUML) |
(Automatic synchronization with BioUML) |
||
| Line 6: | Line 6: | ||
:[[Institute of Systems Biology]] | :[[Institute of Systems Biology]] | ||
;Version | ;Version | ||
| − | :0.9. | + | :0.9.9 |
=== Extension points === | === Extension points === | ||
| Line 22: | Line 22: | ||
*[[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]] [[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]] [[Common and IPS scores correlation (analysis)|Common and IPS scores correlation]] | ||
| + | *[[File:Default-analysis-icon.png]] [[Comparison of RiboSeq data sets by using mRNA features (analysis)|Comparison of RiboSeq data sets by using mRNA features]] | ||
*[[File:Default-analysis-icon.png]] [[Convert files to tracks (analysis)|Convert files to tracks]] | *[[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]] | ||
| Line 42: | Line 45: | ||
*[[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 mRNA fragments (analysis)|Oligonucleotides in mRNA fragments]] | *[[File:Default-analysis-icon.png]] [[Oligonucleotides in mRNA fragments (analysis)|Oligonucleotides in mRNA fragments]] | ||
| Line 50: | Line 55: | ||
*[[File:Default-analysis-icon.png]] [[ROC-curves in grouped peaks (analysis)|ROC-curves in grouped 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]] [[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]] [[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]] [[Ribo-Seq and mRNA features regression (analysis)|Ribo-Seq and mRNA features regression]] | ||
*[[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]] [[Summary on AUCs (analysis)|Summary on AUCs]] | ||
*[[File:Default-analysis-icon.png]] [[Two multivariate sample analysis]] | *[[File:Default-analysis-icon.png]] [[Two multivariate sample analysis]] | ||
Revision as of 12:22, 25 August 2015
- ID
- biouml.plugins.bindingregions
- Name
- Binding-regions related analyses
- Provider
- Institute of Systems Biology
- Version
- 0.9.9
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
- Classification analysis
- Cluster analysis
- Common and IPS scores correlation
- Comparison of RiboSeq data sets by using mRNA features
- 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
- Multivariate regression analysis
- Multivariate sample analysis
- 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
- Regression analysis
- Ribo-Seq and mRNA features forming
- Ribo-Seq and mRNA features regression
- SNP regions in genome
- SNPs in binding regions
- Summary on AUCs
- Two multivariate sample analysis
- lincRNA and mRNA features
