CellRegMap
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limix
CellRegMap: A statistical framework for mapping context-specific regulatory variants using scRNA-seq
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.
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