https://github.com/limix/cellregmap

CellRegMap: A statistical framework for mapping context-specific regulatory variants using scRNA-seq
https://github.com/limix/cellregmap

cellregmap eqtl limix sc-eqtl scrna-seq structlmm

Last synced: 6 months ago
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CellRegMap: A statistical framework for mapping context-specific regulatory variants using scRNA-seq

• Host: GitHub
• URL: https://github.com/limix/cellregmap
• Owner: limix
• License: mit
• Created: 2019-04-02T15:35:25.000Z (about 6 years ago)
• Default Branch: main
• Last Pushed: 2024-08-20T06:26:43.000Z (9 months ago)
• Last Synced: 2024-11-06T00:20:10.225Z (7 months ago)
• Topics: cellregmap, eqtl, limix, sc-eqtl, scrna-seq, structlmm
• Language: Python
• Homepage:
• Size: 11.2 MB
• Stars: 21
• Watchers: 3
• Forks: 3
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# 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](https://www.nature.com/articles/s41588-018-0271-0) 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](https://www.embopress.org/doi/full/10.15252/msb.202110663).

For more instructions and tutorials to facilitate usage of the package visit [our website](https://limix.github.io/CellRegMap/)!

## 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](https://hub.docker.com/r/annasecuomo/cellregmap).