monocle

DOI: 10.18129/B9.bioc.monocle  

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

Bioconductor version: Release (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 uw.edu>

Installation

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

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

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")

 

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

Details

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
SystemRequirements
Enhances
URL
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	monocle_2.26.0.zip
macOS Binary (x86_64)	monocle_2.26.0.tgz
macOS Binary (arm64)	monocle_2.26.0.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