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MGD_playground

This is a place for some simple code that demonstrates models etc. run on the MGD single-cell -omics data.

Why use MouseGastrulationData? It has well annotated:

  • Multi-sample, multi-timepoint scRNA-seq data from the gastrulation atlas
  • Perturbation scRNA-seq data from the chimaeras
  • (soon) scATAC-seq data from E8.25 embryos (with matched scRNA-seq in the atlas)
  • (soon) Spatial transcriptomic data from E8.5 embryos.

all of which can be accessed using ExperimentHub and saved as loom files.

Usage guide/structure

  1. Make the singularity images from images

  2. Prepare the data with get-data scripts

  3. Run the scripts with the relevant image! Scripts for a method are contained in their own folders. The naming should be self-explanatory for images (e.g. bioc.sif is for the R code).

Contributions

If you have a method you would like to demonstrate, please do contribute it here - pull requests are very welcome. Just make a folder that contains the scripts to run your code, and a definition file for a singularity image (or a docker image).