To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("monocle")

In most cases, you don't need to download the package archive at all.

monocle

DOI: 10.18129/B9.bioc.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 (3.7)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("monocle")

Documentation

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

browseVignettes("monocle")

 

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

Details

biocViews Clustering, DataImport, DataRepresentation, DifferentialExpression, GeneExpression, Infrastructure, MultipleComparison, QualityControl, RNASeq, Sequencing, Software, Visualization
Version 2.7.0
In Bioconductor since BioC 3.0 (R-3.1) (3 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, densityClust (>= 0.3), Rtsne, MASS, reshape2, limma, tibble, dplyr, qlcMatrix, pheatmap, stringr, proxy, slam, viridis, stats, biocViews
LinkingTo
Suggests destiny, Hmisc, knitr, Seurat, scater, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me uSORT
Suggests Me scater, scran, sincell
Build Report  

Package Archives

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

Source Package monocle_2.7.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) monocle_2.7.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/monocle
Package Short Url http://bioconductor.org/packages/monocle/
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