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Supporting Next Generation Single-Cell Genomics Experiments with Monocle

Project Monocle
Funding Cycle 3

Proposal Summary

To improve Monocle with algorithms, statistical methods, and web-based visualization tools that will enable biologists using single-cell genomics to extract and disseminate new insights from their experiments.



Monocle is a widely used toolkit for analyzing single cell transcriptome sequencing experiments by biologists interested in identifying new cell types and developmental states and the genes that define them. Over the past five years, dramatic improvements in throughput and sensitivity in single-cell genomics assays from the lab and others have enabled whole organism-scale experiments, large genetic and chemical screens, joint analyses of cells from many different species, and collection of multiple modalities from the same cells. Monocle has continually developed to match these improvements and expand the scope of analyses users can perform. These improvements will position Monocle to serve the biology community’s next generation of single-cell genomics experiments.

Key Personnel

Cole Trapnell