Cell Line Authentication by SNP Profiling (CLASP). (production)
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README.md

clasp

Cell Line Authentication by SNP Profiling (CLASP).

This package supports the publication:

Didion JP et al, 'SNP array profiling of mouse cell lines identifies their strains of origin and reveals cross-contamination and widespread aneuploidy,' BMC Genomics 2014, 15:847, doi:10.1186/1471-2164-15-847.

Installation

Installation requires the devtools package and a couple of BioConductor packages.

Make sure not to build the vignette (set build_vignettes=FALSE, as shown below) unless you want to be waiting for a long time!

# allow BioConductor packages to be installed via install.packages
setRepositories(1:2)
# install devtools
install.packages(‘devtools’)
library(devtools)
# install CLASP and dependencies
devtools::install_github("jdidion/clasp/src/clasp", build_vignettes=FALSE)

Usage

The vignette (vignettes/mouse-cell-lines.pdf) demonstrates how to use CLASP to reproduce the analyses from the paper. Because the vignette takes a very long time to run, it is not a part of the R package.