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

Bioconductor version: Release (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>

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


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

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 2.32.0
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, pheatmap, stringr, proxy, slam, viridis, stats, biocViews, RANN (>= 2.5), Rcpp (>= 0.12.0)
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Suggests destiny, Hmisc, knitr, Seurat, scater, testthat
Linking To Rcpp
Depends On Me cicero
Imports Me uSORT
Suggests Me sincell, grandR, Seurat
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package monocle_2.32.0.tar.gz
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macOS Binary (x86_64) monocle_2.32.0.tgz
macOS Binary (arm64) monocle_2.32.0.tgz
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Source Repository (Developer Access) git clone
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