Monocle is a toolkit for analyzing single-cell gene expression experiments. It was designed for RNA-Seq, but can also work with single cell qPCR. It performs differential expression analysis, and can find genes that differ between cell types or between cell states. When used to study an ongoing biological process such as cell differentiation, Monocle learns that process and places cells in order according to their progress through it. Monocle finds genes that are dynamically regulated during that process.
Cole Trapnell’s lab at the University of Washington.
:: MORE INFORMATION
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.
Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, Lennon NJ, Livak KJ, Mikkelsen TS, Rinn JL.
Nat Biotechnol. 2014 Apr;32(4):381-6. doi: 10.1038/nbt.2859.