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Analysis Tools Registry


Kelly Street, Davide Risso, Diya Das, Sandrine Dudoit, Koen Van den Berge, and Robrecht Cannoodt


Build Status Coverage Status

Slingshot provides functions for inferring continuous, branching lineage structures in low-dimensional data. Designed to model developmental trajectories in single-cell RNA sequencing data, Slingshot can also serve as a component in an analysis pipeline after dimensionality reduction and clustering. It is flexible enough to handle arbitrarily many branching events and allows for the incorporation of prior knowledge through supervised graph construction.


docker pull

How to run Slingshot with SingleCellExperiment object as rds file

curl -L -o slingshot_input.rds
docker run -v ${PWD}:/data -w /data --rm -it Rscript /software/scripts/run_slingshot.R --input=slingshot_input.rds --input-type=rds --reduced-dim=zinbwave

How to run Slingshot with expression matrix and cluster labels as tab delimited files

curl -L -o rd.tsv
curl -L -o cl.tsv
docker run -v ${PWD}:/data -w /data --rm -it Rscript /software/scripts/run_slingshot.R --input= rd.tsv --cluster-labels=cl.tsv --input-type=matrix


Run this command to confirm your container produces correct reference output:

docker run -v ${PWD}:/data -w /data --rm -it Rscript /software/scripts/run_slingshot.R  --validate


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