soedinglab/merlot repository overview

⁠MERLoT: a MEthod for Reconstructing Lineage tree Topologies from scRNA-seq data

MERLot is a tool that can reconstruct the lineage tree topology that explains the emergence of different cell types from a progenitor population. MERLot is an R package than can reconstruct complex lineage tree topologies using coordinates for cells in a given manifold (like diffusion maps) as input.

A small but critical part of MERLoT was written in python; to make installation easier, we created a Docker container with all necessary python libraries.

To use, simply pull the container and then call the calculateScaffoldTree with the docker argument:

scaffold <- CalculateScaffoldTree(coordinates, docker="soedinglab/merlot")

⁠References

Parra et al., bioRxiv, 2018, doi: https://doi.org/10.1101/261768⁠

GitHub repository⁠

Keep posted about MERLoT by following Gonzalo⁠ and Niko⁠ on Twitter.

⁠Troubleshooting

If you just installed Docker, you need to add your user to the docker group in order to have permission to access the unix socket that communicate with the engine. Type sudo usermod -a -G docker $USER in the shell, log out and log back in.

If this doesn't fix it, chances are that the Docker daemon is not running. Try running dockerd (might require sudo priviledges) and try again.