An important update for the HCA community: Major changes are coming soon to the HCA DCP. Read the announcement.

Analysis Tools Registry

Slingshot

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

View

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.

Use

docker pull quay.io/kstreet13/slingshot-docker:1.1.2

How to run Slingshot with SingleCellExperiment object as rds file

curl -L -o slingshot_input.rds https://github.com/kstreet13/slingshot-docker/raw/master/data/slingshot_input.rds
docker run -v ${PWD}:/data -w /data --rm -it quay.io/kstreet13/slingshot-docker:1.1.2 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 https://github.com/kstreet13/slingshot-docker/raw/master/data/rd.tsv
curl -L -o cl.tsv https://github.com/kstreet13/slingshot-docker/raw/master/data/cl.tsv
docker run -v ${PWD}:/data -w /data --rm -it quay.io/kstreet13/slingshot-docker:1.1.2 Rscript /software/scripts/run_slingshot.R --input= rd.tsv --cluster-labels=cl.tsv --input-type=matrix

Validate

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

docker run -v ${PWD}:/data -w /data --rm -it quay.io/kstreet13/slingshot-docker:1.1.2 Rscript /software/scripts/run_slingshot.R  --validate

Contact

Kelly Street (street.kelly@gmail.com)

Improve this page