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Bioconductor - monocle

monocle

This is the released version of monocle; for the devel version, see monocle.

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

Bioconductor version: Release (3.21)

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 (version "4.5") 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 PDF R Script Reference Manual PDF NEWS Text Details biocViews Clustering, DataImport, DataRepresentation, DifferentialExpression, GeneExpression, ImmunoOncology, Infrastructure, MultipleComparison, QualityControl, RNASeq, Sequencing, Software, Visualization Version 2.36.0 In Bioconductor since BioC 3.0 (R-3.1) (10.5 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, pheatmap, stringr, proxy, slam, viridis, stats, biocViews, RANN (>= 2.5), Rcpp (>= 0.12.0) System Requirements URL See More Package Archives

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

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