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:

• 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
• 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