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Monocle

Allows to analyze single-cell gene expression experiments. Monocle can realize differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. The software orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well. The tools Census and BEAM are implemented in Monocle.

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Monocle classification

Monocle specifications

Software type:
Toolkit/Suite
Restrictions to use:
None
License:
Artistic License version 2.0
Version:
2.4.0
Requirements:
methods, Matrix, Biobase, ggplot2, VGAM, DDRTree
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes

Subtools

  • Census
  • BEAM

Monocle distribution

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Monocle support

Documentation

Maintainer

  • Cole Trapnell <>

Credits

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Publications

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

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.

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.