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gitter-lab / SINGE

Gene regulatory network reconstruction from pseudotemporal single-cell gene expression data
MIT License
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Automating SINGE for branching trajectories #49

Closed atuldeshpande closed 4 years ago

atuldeshpande commented 4 years ago

We should investigate strategies to automate the workflow of splitting a branching trajectory into multiple cell-fate based subdirectories, followed by SINGE analysis on each subdirectory and obtaining GRNs based on these analyses. Some initial thoughts are provided in USAGE.md.

chenxofhit commented 4 years ago

I think this is a very complex problem. A future work is to judge the bifurcation interval rather than a whole trajectory, with only a few but important genes considered.

agitter commented 4 years ago

It is definitely a complex problem. @atuldeshpande is working on pull request #57 that will bring major improvements for running SINGE on branching trajectories. Our approach is to add support for indicator variables for each cell so that only the cell corresponding to a particular branch or path can be selected. SINGE will then run automatically on all user-defined branches. We'll also add an example showing how to create the branch indicator data structure with the output from dynverse.

That will provide a way to run SINGE on the bifurcation interval instead of the whole trajectory. SINGE does not do any gene selection. A user should decide which genes are important using an appropriate statistical test or external criteria before running SINGE.