TF-COMB

TF-COMB stands for "Transcription Factor Co-Occurrence using Market Basket analysis" and is a python module for identifying co-occurring TFs in regulatory regions. Additionally, TF-COMB applies various downstream methods such as distance, orientation and network analysis.

The source code is located at: https://github.com/loosolab/TF-COMB

Contents of this documentation

• Install
• Examples
  • ChIP-seq analysis
  • TFBS from motifs
  • Selection of rules
  • Network analysis
  • Orientation analysis
  • Annotate binding sites to genes
  • Differential analysis
  • Binding distance analysis
  • GO-term analysis
  • Genomic locations of TF-TF pairs
  • Plot TFBS in genome view
  • Plot footprints for TF pair locations
• Methods
  • Adopted Market Basket Analysis (adopted MBA)
  • Anchor Modes
• API reference
  • tfcomb.objects module
  • tfcomb.network module
  • tfcomb.analysis module
  • tfcomb.annotation module
  • tfcomb.plotting module
  • tfcomb.utils module
• Changelog
  • 1.1 (11-08-2023)
  • 1.0.3 (23-01-2023)
  • 1.0.2 (20-01-2023)
  • 1.0.1 (24-11-2022)
  • 1.0.0 (25-10-2022)