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.

Monocle was written by Cole Trapnell with input from Davide Cacchiarelli.

Papers

Cicero predicts cis-regulatory DNA interactions from single-cell chromatin accessibility data

A single-cell atlas of in vivo mammalian chromatin accessibility

The cis-regulatory dynamics of embryonic development at single-cell resolution

Reversed graph embedding resolves complex single-cell trajectories

Aligning single-cell developmental and reprogramming trajectories identifies molecular determinants of reprogramming outcome

Single-cell mRNA quantification and differential analysis with Census

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells