README.Rmd

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# iceqream <img src="man/figures/logo.png" align="right" height="280" alt="" />

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[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
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`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](man/figures/pipeline.png)

## Installation

You can install the development version of iceqream like so:

``` r
remotes::install_github("tanaylab/iceqream")
```

## Usage 

See the [vignette](https://tanaylab.github.io/iceqream/articles/iceqream.html) for a detailed example on a mouse gastrulation trajectory.