Bioconductor version: Release (3.6)
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")
):
To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("monocle")
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("monocle")
R Script | Monocle: Cell counting, differential expression, and trajectory analysis for single-cell RNA-Seq experiments | |
Reference Manual | ||
Text | README | |
Text | NEWS |
biocViews | Clustering, DataImport, DataRepresentation, DifferentialExpression, GeneExpression, Infrastructure, MultipleComparison, QualityControl, RNASeq, Sequencing, Software, Visualization |
Version | 2.6.4 |
In Bioconductor since | BioC 3.0 (R-3.1) (3.5 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 |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | monocle_2.6.4.tar.gz |
Windows Binary | monocle_2.6.4.zip (32- & 64-bit) |
Mac OS X 10.11 (El Capitan) | monocle_2.6.4.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/monocle |
Package Short Url | http://bioconductor.org/packages/monocle/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.6 | Source Archive |
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