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.
iceqream-pipeline
Installation
You can install the development version of iceqream like so:
remotes::install_github("tanaylab/iceqream")Usage
See the vignette for a detailed example on a mouse gastrulation trajectory.