Package: monocle
Type: Package
Title: Clustering, differential expression, and trajectory analysis for
        single- cell RNA-Seq
Version: 2.41.0
Date: 2024-03-13
Author: Cole Trapnell
Maintainer: Cole Trapnell <coletrap@uw.edu>
Description: 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.
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)
LinkingTo: Rcpp
Suggests: destiny, Hmisc, knitr, Seurat, scater, testthat
VignetteBuilder: knitr
Roxygen: list(wrap = FALSE)
LazyData: true
biocViews: ImmunoOncology, Sequencing, RNASeq, GeneExpression,
        DifferentialExpression, Infrastructure, DataImport,
        DataRepresentation, Visualization, Clustering,
        MultipleComparison, QualityControl
Packaged: 2026-06-23 16:06:40 UTC; root
RoxygenNote: 7.3.1
Config/pak/sysreqs: libglpk-dev make libicu-dev libxml2-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:39:09 UTC
RemoteUrl: https://github.com/bioc/monocle
RemoteRef: HEAD
RemoteSha: 733301c2e146e2e3b34f9a621694fec69896adb0
NeedsCompilation: yes