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 (3.24)
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("monocle")):Cole Trapnell. monocle: Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq. doi:10.18129/B9.bioc.monocle, R package version 2.41.0, https://bioconductor.org/packages/monocle.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, DataImport, DataRepresentation, DifferentialExpression, GeneExpression, ImmunoOncology, Infrastructure, MultipleComparison, QualityControl, RNASeq, Sequencing, Software, Visualization |
| Version | 2.41.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (12 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 |
| Imports Me | uSORT |
| Suggests Me | ClusterGVis, Seurat, sincell |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | monocle_2.41.0.tar.gz |
| Windows Binary (x86_64) | monocle_2.41.0.zip |
| macOS Binary (big-sur-x86_64) | monocle_2.41.0.tgz |
| macOS Binary (sonoma-arm64) | monocle_2.41.0.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 | https://bioconductor.org/packages/monocle/ |
| Package Downloads Report | Download Stats |