Analysis of Binding Regions (analysis)

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Analysis title
Default-analysis-icon.png 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
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