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.

For more instructions and tutorials to facilitate usage of the package visit our website!

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.

Installation using a Docker image

If you use Docker, you can also pull the pre-build image from dockerhub.

<!-- ## Running tests From your command line, enter python3 setup.py test --> <!-- ## Project layout ├─ old_files/ old scripts ├─ references/ documents on the mathematical concepts └─ CellRegMap/ package implementation └─ test/ test file ## References - [Exploring Multivariate Gene-Environment Interactions: Models And Applications](https://www.repository.cam.ac.uk/handle/1810/290971) - [Optimal tests for rare variant effects in sequencing association studies](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3440237/) [Supplementary material](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3440237/bin/supp_kxs014_kxs014supp.pdf) -->