iceqream (Interpretable Computational Engine for Quantitative Regression of Enhancer ATAC Motifs, in short: IQ) is a package for regressing accessibility from sequences using physical models of TF binding.
It models TF effective concentrations as latent variables that activate or repress regulatory elements in a nonlinear fashion, with possible contribution from pairwise interactions and synergistic chromosomal domain effects. IQ allows inference and synthesis of models explaining accessibility dynamics over an entire single cell manifold.
You can install the development version of iceqream like so:
remotes::install_github("tanaylab/iceqream")See the vignette for a detailed example on a mouse gastrulation trajectory.