monocle
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Bioconductor version: Release (3.17)
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")):
Installation
To install this package, start R (version "4.3") 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")| 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 | 2.28.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (9 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) |
| Linking To | Rcpp |
| Suggests | destiny, Hmisc, knitr, Seurat, scater, testthat |
| System Requirements | |
| Enhances | |
| URL |
See More
| Depends On Me | cicero, 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_2.28.0.tar.gz |
| Windows Binary | monocle_2.28.0.zip |
| macOS Binary (x86_64) | monocle_2.28.0.tgz |
| macOS Binary (arm64) | monocle_2.28.0.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 |