Bisaloo/RBPEqBind

RBPEqBind simulates competitive binding of multiple RNA-binding proteins (RBPs) to RNA sequences using equilibrium binding kinetics.

# Install devtools if needed
if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")

devtools::install_github("S00NYI/RBPEqBind")

library(RBPEqBind)

# Load and process RBP models
raw_models <- loadModel("model.csv")
rbp_models <- setModel(raw_models, max_affinity = 100)

# Run simulation
results <- simulateBinding(
  sequence = "ACGUACGUACGU...",
  rbp_models = rbp_models,
  protein_concs = c(RBP1 = 100, RBP2 = 100),
  rna_conc = 10
)

# Visualize
plotBinding(results, rbp = c("RBP1", "RBP2"))

• Competitive binding simulation for multiple RBPs
• Concentration grid sweeps for parameter exploration
• FASTA file support for transcriptome-wide analysis
• Visualization with binding profiles, heatmaps, and bubble plots

See the package vignette for detailed examples covering:

1. Single sequence simulation
2. Concentration grid sweeps
3. FASTA file processing
4. Visualization options

For detailed usage, see Figure_Scripts folder in: https://github.com/S00NYI/BITS_Specificity

If you use RBPEqBind in your research, please cite:

Yi S, Singh SS, Ye X, Krishna R, Jankowsky E, Luna JM. (2025). Inherent Specificity and Mutational Sensitivity as Quantitative Metrics for RBP Binding. bioRxiv. https://www.biorxiv.org/content/10.1101/2025.03.28.646018v2

This package was developed in part with Google Antigravity.

For the original R implementation of RBP simulation analysis, see Deprecated folder in: https://github.com/S00NYI/BITS_Specificity