Analysis of Binding Regions (analysis)

Analysis title

Analysis of Binding Regions

Provider

Institute of Systems Biology

Class

BindingRegions

Plugin

biouml.plugins.bindingregions (Binding-regions related analyses)

Parameters:

• MODE – MODE defines the concrete session of given analysis.
• Exp parameters1 – Exp parameters1
  • Path to Genome Sequences – Path to Genome Sequences
• Exp parameters2 – Exp parameters2
  • Path to Outputs – Path to Outputs
• Exp parameters3 – Exp parameters3
  • Path to input tracks – Path to input tracks
• Exp parameters4 – Exp parameters4
  • Specie – Specie
• Exp parameters5 – Exp parameters5
  • Path to Auxiliary Tables – Path to Auxiliary Tables
• Exp parameters6 – Exp parameters6
  • Path to Single Input Track – Path to Single Input Track
• Exp parameters7 – Exp parameters7
  • tfClass – Class of Transcription Factor
• Exp parameters8 – Exp parameters8
  • Path to SiteModel – Path to SiteModel
• Exp parameters9 – Exp parameters9
  • Path to Inputs – Path to Inputs
• Exp parameters10 – Exp parameters10
  • Path to Matrices – Path to Matrices
• Exp parameters11 – Exp parameters11
  • Path to Matrix – Path to Matrix
• Exp parameters12 – Exp parameters12
  • Minimal Number of Overlaps – Minimal Number of Overlaps
• Exp parameters13 – Exp parameters13
  • Number of mixture components – Number of mixture components
• Exp parameters14 – Exp parameters14
  • p_value – p_value
• Exp parameters15 – Exp parameters15
  • Path to Collection of creating matrices – Path to Collection of creating matrices
• Exp parameters16 – Exp parameters16
  • Base Name of Creating Matrices – Base Name of Creating Matrices
• Exp parameters17 – Exp parameters17
  • Maximal Number of Iterations – Maximal Number of Iterations
• Exp parameters18 – Exp parameters18
  • Number of Matrices Will Be Constructed – Number of Matrices Will Be Constructed
• Exp parameters19 – Exp parameters19
  • consensus – consensus
• Exp parameters20 – Exp parameters20
  • isInitialMatrixGivenByConsensus – is initial matrix given by consensus? (true or false)
• Exp parameters21 – Exp parameters21
  • oligLength – length of oligs
• Exp parameters22 – Exp parameters22
  • IPS threshold – IPS threshold
• Exp parameters23 – Exp parameters23
  • Percentage of Best Sites – Percentage of Best Sites
• Exp parameters24 – Exp parameters24
  • toRemoveAlu – Do you want to remove Alu-repeats? (true or false)
• Exp parameters25 – Exp parameters25
  • isLogTransformation – Do you want to consider log-models? (true or false)
• Exp parameters27 – Exp parameters27
  • isAroundSummit – is around summit? (true or false)
• Exp parameters28 – Exp parameters28
  • Path to ChIP-Seq Track – Path to ChIP-Seq Track
• Exp parameters29 – Exp parameters29
  • minimal length of sequence region – minimal length of sequence region
• Exp parameters30 – Exp parameters30
  • Path to input tracks2 – Path to input tracks2