Analysis Tools Registry
Single-cell consensus clustering (SC3)
SC3 is an unsupervised clustering method for scRNA-seq data. SC3 also estimates the number of clusters and it provides features to aid the biological interpretation of the clusters. sc3-scripts provides a set of simple wrappers with robust argument parsing for individual components of the SC3 package.
Use
docker pull quay.io/biocontainers/bioconductor-sc3-scripts:0.0.3--r351_0How to perform unsupervised clustering on scRNA-seq data (already QCed and normalised) in a SingleCellExperiment object
curl -L -o deng-reads.rds https://github.com/hemberg-lab/scRNA.seq.course/raw/master/deng/deng-reads.rds
curl -L -o sc3-sc3.R https://raw.githubusercontent.com/ebi-gene-expression-group/bioconductor-sc3-scripts/develop/sc3-sc3.R
docker run -v ${PWD}:/data -w /data --rm quay.io/biocontainers/bioconductor-sc3-scripts:0.0.3--r351_0 Rscript sc3-sc3.R -i deng-reads.rds -o deng-sc3.rds Validate
Run this command to confirm your container produces correct reference output:
curl -L -o sc3-sc3-validate.R https://raw.githubusercontent.com/ebi-gene-expression-group/bioconductor-sc3-scripts/develop/sc3-sc3-validate.R
docker run -v ${PWD}:/data -w /data --rm quay.io/biocontainers/bioconductor-sc3-scripts:0.0.3--r351_0 Rscript sc3-sc3-validate.RContact
Martin Hemberg, SC3 (mh26@sanger.ac.uk)
Gene Expression Team, sc3-scripts (gene-expression@ebi.ac.uk)
