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. | + | :0.9.8 |
=== Extension points === | === Extension points === | ||
Line 17: | Line 17: | ||
*[[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