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monocle

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")):

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("monocle")

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

Documentation

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

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

Details

biocViews Clustering, DataImport, DataRepresentation, DifferentialExpression, GeneExpression, ImmunoOncology, Infrastructure, MultipleComparison, QualityControl, RNASeq, Sequencing, Software, Visualization
Version 2.31.1
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)
System Requirements
URL
See More
Suggests destiny, Hmisc, knitr, Seurat, scater, testthat
Linking To Rcpp
Enhances
Depends On Me cicero, phemd
Imports Me uSORT
Suggests Me sincell
Links To Me
Build Report Build Report

Package Archives

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

Source Package monocle_2.31.1.tar.gz
Windows Binary monocle_2.31.1.zip
macOS Binary (x86_64) monocle_2.31.1.tgz
macOS Binary (arm64) monocle_2.31.1.tgz
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/
Package Downloads Report Download Stats