Code for "A complete map of specificity encoding enables reprogramming of a protein interaction" by Taraneh Zarin, Cristina Hidalgo-Carcedo and Ben Lehner (https://www.biorxiv.org/content/10.1101/2024.04.25.591103v3)
Please download and untar/unzip the required data directory from https://zenodo.org/records/21827986 (version 2; updated from: https://zenodo.org/records/11048045 to include reprogramming data and modelling results)
Create a parent directory that contains the data directory above and the fuzzy_specificity_code directory provided here (https://github.com/lehner-lab/fuzzy_specificity/).
This code was last run and tested on: R version 4.3.1 (2023-06-16 ucrt)
The following packages and were loaded during the test run (format: package_version):
circlize_0.4.15
data.table_1.17.0
cowplot_1.1.1
seqinr_4.2-30
viridis_0.6.2
viridisLite_0.4.1
ggpubr_0.6.0
GGally_2.1.2
ggseqlogo_0.1
stringr_1.5.0
ggplot2_4.0.1
ComplexHeatmap_2.15.3