SIMLR: A Tool for Large-Scale Genomic Analyses by Multi-Kernel Learning

Bo Wang, Daniele Ramazzotti, Luca De Sano, Junjie Zhu, Emma Pierson, Serafim Batzoglou
2018 Proteomics  
We here present SIMLR (Single-cell Interpretation via Multi-kernel LeaRning), an open-source tool that implements a novel framework to learn a sample-to-sample similarity measure from expression data observed for heterogenous samples. SIMLR can be effectively used to perform tasks such as dimension reduction, clustering, and visualization of heterogeneous populations of samples. SIMLR was benchmarked against state-of-the-art methods for these three tasks on several public datasets, showing it
more » ... be scalable and capable of greatly improving clustering performance, as well as providing valuable insights by making the data more interpretable via better a visualization. Availability and Implementation SIMLR is available on GitHub in both R and MATLAB implementations. Furthermore, it is also available as an R package on http://bioconductor.org.
doi:10.1002/pmic.201700232 pmid:29265724 fatcat:duktczfimvfqbaaovbjofb5x2m