STARE - Look into TF regulation on gene level leveraging an adapted Activity-By-Contact score

• Gettings started
  • Installing STARE
  • Get started and test runs
  • Input and options
    • Required input
    • Other input options
      • -b / --bed_file
      • -n / --column
      • -f / --contact_folder
      • -r / --existing_abc
  • Output
    • ABC output
    • Gene-TF-matrices
    • Output per activity column (-n)
  • Computational power and parallelisation
  • Separate ABC-scoring
• PSCMs and PSEMs
• Affinity summarisation
  • Gene window
  • ABC-scoring
  • Not-adapted ABC-scoring
• Binary output
  • ExampleOutput_Reshape_Binary.bin.gz and ExampleOutput_Reshape_Meta.txt
  • Byte-order / Endianness
• Patch notes
  • v1.0.5
  • v1.0.4
  • v1.0.3
  • v1.0.2
  • v1.0.1
• Troubleshooting
  • Index of activity columns
  • Header in bed-files
  • Gene annotation and gene IDs
  • The chr prefix
  • Is it compressed?
  • Still not working?
• References