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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




No version available



  • person_outline Cole Trapnell

Additional information

Publications for Monocle

Monocle citations


Parental haplotype specific single cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells

Nat Commun
PMCID: 5951918
PMID: 29760424
DOI: 10.1038/s41467-018-04215-7

[…] her expression levels compared to mean of the other groups combined were determined (pair-wise analysis). The complete list of enriched genes by fetal age and by germ cell stage (Supplementary Data ).Monocle analysis: To rank the 129 female germ cells by their maturation status, we utilized the R implementation of Monocle in Bioconductor. We selected genes with >5 TPM in at least 4 cells. That set […]


Characterization of germ cell differentiation in the male mouse through single cell RNA sequencing

Sci Rep
PMCID: 5916943
PMID: 29695820
DOI: 10.1038/s41598-018-24725-0
call_split See protocol

[…] scrat, Seurat). As none of these led to the exclusion of more than 5 cells even at stringent settings, no further filtering of cells was performed.Pseudotime analysis was performed using the scater, monocle– and scrat– packages for R.RNA half-life was calculated by applying a LOESS regression to total counts per cell for each sex chromosome and the total of all autosomes divided by the respective […]


Using single‐cell genomics to understand developmental processes and cell fate decisions

Mol Syst Biol
PMCID: 5900446
PMID: 29661792
DOI: 10.15252/msb.20178046

[…] cher may prefer to use a method that summarises the continuity of cell states in the data.Such methods are typically referred to as pseudotime methods, a term first introduced by the software package Monocle (Trapnell et al, ). Pseudotime describes an ordering of cells according to some characteristic in the data; this may represent developmental processes occurring over time, or the effects of co […]


Molecular transitions in early progenitors during human cord blood hematopoiesis

Mol Syst Biol
PMCID: 5852373
PMID: 29545397
DOI: 10.15252/msb.20178041

[…] al leaves (Figs B and E). For the hierarchical relationships relating HSC to four downstream fates, we obtained identical results in 100% of the 500 bootstraps. We also obtained similar results using Monocle, which performs dimensionality reduction using independent components analysis, demonstrating that our results were robust across low‐dimensional representations of the data (Fig F). However, […]


Single cell RNA seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesis

Genome Biol
PMCID: 5853091
PMID: 29540203
DOI: 10.1186/s13059-018-1416-2

[…] re divided into five further clusters (Additional file : Figure S7a and S7b). They developed from cells with a dermomyotome feature (cluster 1) in two directions as revealed by pseudotime analysis in Monocle2 (Additional file : Figure S7a). One was myotome muscle cells (cluster 3), and the other was mesenchymal sclerotomes (cluster 5). The first cluster consisted of cells from E9.5 somites with de […]


Single Cell Computational Strategies for Lineage Reconstruction in Tissue Systems

PMCID: 5924749
PMID: 29713661
DOI: 10.1016/j.jcmgh.2018.01.023

[…] s, and their connections approximate the geometric shape of the data cloud when laid out in 2 dimensions. Multiple MST algorithms (eg, Spanning-tree Progression Analysis of Density-normalized Events, Monocle1, Tools for Single Cell ANalysis, Waterfall) exist and they differ by their applications on different experimental platforms, and the type and degree of clustering of data that occurs before M […]


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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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