Monocle protocols

Monocle computational protocol

Monocle specifications


Unique identifier OMICS_07026
Name Monocle
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 2.8.0
Stability Stable
methods, Matrix, Biobase, ggplot2, VGAM, DDRTree
Maintained Yes


  • BEAM
  • Census
  • detectGenes



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  • person_outline Cole Trapnell <>

Additional information

Publications for Monocle

Monocle IN pipeline

PMCID: 5723634
PMID: 29225342
DOI: 10.1038/s41467-017-02001-5

[…] diffusion map algorithm was robust to the choice of features and down-sampling of cells (supplementary fig. 5b). the structure of a common origin and the two branches could also be inferred using monocle with standard settings48 (supplementary fig. 5a). for inferring the branches and pseudotime ordering, we defined the following three tips, the cell with the largest value for the second […]

Monocle institution(s)
Department of Genome Sciences, University of Washington, Seattle, WA, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA; Department of Applied Mathematics, University of Washington, Seattle, WA, USA
Monocle funding source(s)
Supported by US National Institutes of Health (NIH) grant DP2 HD088158, partly supported by a Dale. F. Frey Award for Breakthrough Scientists and an Alfred P. Sloan Foundation Research Fellowship and a National Science Foundation (NSF) Graduate Research Fellowship.

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