DOI: 10.18129/B9.bioc.monocle  

This package is for version 3.16 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: 3.16

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>

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


To install this package, start R (version "4.2") and enter:

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


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:



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


biocViews Clustering, DataImport, DataRepresentation, DifferentialExpression, GeneExpression, ImmunoOncology, Infrastructure, MultipleComparison, QualityControl, RNASeq, Sequencing, Software, Visualization
Version 2.26.0
In Bioconductor since BioC 3.0 (R-3.1) (8.5 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)
LinkingTo Rcpp
Suggests destiny, Hmisc, knitr, Seurat, scater, testthat
Depends On Me cicero, ctgGEM, phemd
Imports Me uSORT
Suggests Me M3Drop, scran, sincell
Links To Me
Build Report  

Package Archives

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

Source Package monocle_2.26.0.tar.gz
Windows Binary
macOS Binary (x86_64) monocle_2.26.0.tgz
macOS Binary (arm64) monocle_2.26.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: