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This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see monocle.

Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

Bioconductor version: 3.4

Monocle performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle also performs differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.

Author: Cole Trapnell

Maintainer: Cole Trapnell <coletrap at>

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PDF R Script Monocle: Differential expression and time-series analysis for single-cell RNA-Seq and qPCR experiments.
PDF   Reference Manual
Text   NEWS


biocViews Clustering, DataImport, DataRepresentation, DifferentialExpression, GeneExpression, Infrastructure, MultipleComparison, QualityControl, RNASeq, Sequencing, Software, Visualization
Version 2.2.0
In Bioconductor since BioC 3.0 (R-3.1) (2.5 years)
License Artistic-2.0
Depends R (>= 2.10.0), methods, Matrix (>= 1.2-6), Biobase, ggplot2 (>= 1.0.0), VGAM (>= 1.0-1), DDRTree (>= 0.1.4)
Imports parallel, igraph (>= 1.0.1), BiocGenerics, HSMMSingleCell(>= 0.101.5), plyr, cluster, combinat, fastICA, grid, irlba (>= 2.0.0), matrixStats, MASS, reshape2, limma, dplyr, qlcMatrix, pheatmap, stringr, proxy, slam, stats
Suggests knitr, Hmisc, testthat
Depends On Me
Imports Me uSORT
Suggests Me scater, scran, sincell
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