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This is the development version of monocle; for the stable release version, see monocle.

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

Bioconductor version: Development (3.19)

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 uw.edu>

Citation (from within R, enter citation("monocle")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Monocle: Cell counting, differential expression, and trajectory analysis for single-cell RNA-Seq experiments PDF R Script
Reference Manual PDF


biocViews Clustering, DataImport, DataRepresentation, DifferentialExpression, GeneExpression, ImmunoOncology, Infrastructure, MultipleComparison, QualityControl, RNASeq, Sequencing, Software, Visualization
Version 2.31.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License Artistic-2.0
Depends R (>= 2.10.0), methods, Matrix (>= 1.2-6), Biobase, ggplot2 (>= 1.0.0), VGAM (>= 1.0-6), 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, Rtsne, MASS, reshape2, leidenbase (>= 0.1.9), limma, tibble, dplyr, qlcMatrix, pheatmap, stringr, proxy, slam, viridis, stats, biocViews, RANN (>= 2.5), Rcpp (>= 0.12.0)
System Requirements
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Suggests destiny, Hmisc, knitr, Seurat, scater, testthat
Linking To Rcpp
Depends On Me cicero, phemd
Imports Me uSORT
Suggests Me M3Drop, scran, sincell
Links To Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package monocle_2.31.0.tar.gz
Windows Binary monocle_2.31.0.zip
macOS Binary (x86_64) monocle_2.31.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/monocle
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/monocle
Bioc Package Browser https://code.bioconductor.org/browse/monocle/
Package Short Url https://bioconductor.org/packages/monocle/
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