Difference between revisions of "Biouml.plugins.bindingregions (plugin)"

Revision as of 19:02, 13 February 2017

ID

biouml.plugins.bindingregions

Name

Binding-regions related analyses

Provider

Institute of Systems Biology

Version

0.9.10

Extension points

Extension points defined in this plugin:

• biouml.plugins.bindingregions.siteModelFactory

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
• 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
• 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