CellRegMap

Cellular Regulatory Map (CellRegMap) is a linear mixed model approach to perform multi-context eQTL mapping by leveraging single cell RNA sequencing (scRNA-seq) data. It is related to the previously proposed StructLMM but importantly it can account for sample structure, including population structure and repeated observations for the same samples, e.g., multiple cells for the same donor.

The CellRegMap model and its applications to both real and simulated data are described in the CellRegMap manuscript.

We are working on more instructions and tutorials to facilitate usage of the package at this link!

Install

From your command line, enter

python3 -m pip install cellregmap

in your command line.

Development

To install it in development mode, enter

git clone https://github.com/limix/CellRegMap.git
cd CellRegMap
python3 -m pip install -e .

in your command line.

Running tests

From your command line, enter

python3 setup.py test