Welcome to tfbs_footprinting’s documentation!

Contents:

• 1. Introduction
  • 1.1 Basics
  • 1.2 Experimental data
  • 1.3 Ensembl transcript-ids
• 2. Installation
  • 2.1 Pypi installation
  • 2.2 Docker installation
  • 2.3 Requirements
• 3. Input
  • 3.1: CSV of Ensembl transcript IDs and arguments
  • 3.2: Text file of IDs
  • 3.3: Text file TF IDs
• 4. Output
  • 4.1 Promoter Figure
  • 4.2 Table of predictions
  • 4.2 Addtional outputs
• 5. Examples
  • 5.1 TFBS_footprinter Use Examples
  • 5.2 TFBS_footprinter Use Examples Within Docker
  • 5.3 Update experimental data files
• 6. Arguments
• 7. Process
  • 7.1 Steps
  • 7.2 Flowchart
• 8. Species
  • 8.1 Ensembl
  • 8.2 Species table
• 9. Troubleshooting
  • 9.1 Log file
  • 9.1 Docker

Indices and tables

• Index
• Module Index
• Search Page