Examples

The usage of TF-comb is split into three main parts:

1. Setting up the Transcription Factor Binding Sites (TFBS) to use in the analysis

2. Counting co-occurrences and performing market basket analysis

3. Visualization of results and downstream analysis such as network analysis

List of example notebooks:

• 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