monocle

DOI: 10.18129/B9.bioc.monocle    

This package is for version 3.7 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: 3.7

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 2.8.0
In Bioconductor since BioC 3.0 (R-3.1) (4 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, RANN (>= 2.5), Rcpp (>= 0.12.0)
LinkingTo Rcpp
Suggests destiny, Hmisc, knitr, Seurat, scater, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me uSORT
Suggests Me scater, scran, sincell
Links To Me
Build Report  

Package Archives

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

Source Package monocle_2.8.0.tar.gz
Windows Binary monocle_2.8.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) monocle_2.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/monocle
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/monocle
Package Short Url http://bioconductor.org/packages/monocle/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

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