Authors: Shaoxun Liu, Pilar Gomez-Alcala, Christ Leemans, William J. Glassford, Lucas A.N. Melo, Richard S. Mann, Harmen J. Bussemaker

📄 Publication: Nucleic Acids Research (2025)
🧬 Lab Website: The Bussemaker Lab

To reproduce the analysis, you must install the FamilyCode package from GitHub.

# Install devtools if you haven't already
if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")

# Install FamilyCode
devtools::install_github('BussemakerLab/FCpackage')

# Load the library
library(FamilyCode)

Before running the processing scripts, you must acquire the raw data.

1. Download: Visit CisBP (v3.00).
2. Select Family: Choose "bHLH" or "Homeodomain" (download one family at a time).
3. Select Options: Check the boxes for "Z-score" and "TF info".
4. Download: Click the "Download Family Archive" button.
5. Setup: * Uncompress the ZIP files.
   • Place Zscores.txt into the corresponding rawData/HD/ or rawData/bHLH/ directories.

Note: In case of CisBP updates that cause parsing issues, we have provided working versions of Zscores.txt and TF_Information.txt (bHLH: Jan 2019, HD: Jun 2024).

To reproduce the figures from the paper using pre-computed data:

• Script: FamilyCodeFigures.Rmd
• Description: This script uses pre-computed files located in the intermediateData folder.

If you wish to regenerate the intermediate data from scratch, please run the processing scripts below.

Run the following R Markdown files to process raw input data (SELEX-seq or PBM) and perform FamilyCode predictions.