Cell Line Authentication by SNP Profiling
R Package: CLASP
I helped to develop an Illumina genotyping array for the mouse called MegaMUGA. We used this array to genotype a large number of laboratory strains and also cell lines derived from those strains. I developed an R package to build a database from the genotype data (both raw intensities and genotype calls) and use that data to develop an optimized assay for validating the genetic background of the cell lines. The package also estimates cross-contamination and copy number.
- Didion, J. P. et al. SNP array profiling of mouse cell lines identifies their strains of origin and reveals cross-contamination and widespread aneuploidy. BMC Genomics 15, 847 (2014).
I created what I think is a really nice RSS parser library for Ruby, called FeedMe. It is based on regular expressions, which means it is very flexible, although not as fast as other RSS libraries.
Note that this code is ~5 years old and was only tested on Ruby 1.x. Please file issues if you find any.If you liked this post, you can share it with your followers or follow me on Twitter!