Package: monocle3
Title: Clustering, Differential Expression, and Trajectory Analysis for
        Single-Cell RNA-Seq
Version: 1.4.26
Authors@R: c(
    person(given = "Hannah",
           family = "Pliner",
           role = c("aut"),
           email = "hpliner@uw.edu"),
    person(given = "Xiaojie",
           family = "Qiu",
           role = c("aut"),
           email = "xqiu@uw.edu"),
    person(given = "Cole",
           family = "Trapnell",
           role = c("aut"),
           email = "coletrap@uw.edu"),
    person(given = "Brent",
           family = "Ewing",
           role = c("cre"),
           email = "bge@uw.edu"))
Description: Monocle 3 performs clustering, differential expression and 
    trajectory 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 3 also performs differential expression analysis, 
    clustering, visualization, and other useful tasks on single-cell expression 
    data.  It is designed to work with RNA-Seq data, but could be used with 
    other types as well.
biocViews: Software, SingleCell, RNASeq, ATACSeq, Normalization,
        Preprocessing, DimensionReduction, Visualization,
        QualityControl, Clustering, Classification, Annotation,
        GeneExpression, DifferentialExpression
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
LinkingTo: Rcpp
Depends: R (>= 4.0.0), Biobase, SingleCellExperiment
Imports: assertthat (>= 0.2.1), batchelor, BiocGenerics (>= 0.28.0),
        BiocParallel, BPCells, DelayedArray (>= 0.8.0),
        DelayedMatrixStats (>= 1.4.0), digest (>= 0.6.28), dplyr (>=
        0.8.0.1), future (>= 1.23.0), ggdist (>= 3.3.0), ggforce (>=
        0.4.1), ggplot2 (>= 3.1.1), ggrastr, ggrepel (>= 0.8.1), grr,
        HDF5Array, igraph (>= 1.5.0), irlba (>= 2.3.3), leidenbase (>=
        0.1.25), limma (>= 3.38.3), lme4 (>= 1.1-27), lmtest (>=
        0.9-36), MASS (>= 7.3-51.4), Matrix (>= 1.2-17), methods,
        openssl, pbapply (>= 1.4-0), pbmcapply (>= 1.4.1), pheatmap,
        plotly (>= 4.9.0), plyr (>= 1.8.4), proxy (>= 0.4-23), pscl (>=
        1.5.2), purrr (>= 0.3.2), RANN (>= 2.6.1), RColorBrewer, Rcpp
        (>= 1.0.1), reshape2 (>= 1.4.3), rsample (>= 0.0.5),
        RhpcBLASctl, RcppAnnoy, RcppHNSW (>= 0.3.0), Rtsne (>= 0.15),
        S4Vectors, sf, shiny, slam (>= 0.1-45), spdep (>= 1.1-2),
        speedglm (>= 0.3-2), stats, stringr (>= 1.4.0),
        SummarizedExperiment (>= 1.11.5), utils, uwot (>= 0.1.8),
        tibble (>= 2.1.1), tidyr (>= 0.8.3), viridis (>= 0.5.1)
Suggests: knitr, pryr (>= 0.1.4), rmarkdown, scran, spelling, testthat
        (>= 2.1.0)
Remotes: github::bnprks/BPCells/r, github::cole-trapnell-lab/speedglm
VignetteBuilder: knitr
Language: en-US
NeedsCompilation: yes
Packaged: 2022-05-10 17:21:53 UTC; brent
Maintainer: Brent Ewing <bge@uw.edu>
Author: Hannah Pliner [aut],
  Xiaojie Qiu [aut],
  Cole Trapnell [aut],
  Brent Ewing [cre]
Built: R 4.4.3; x86_64-conda-linux-gnu; 2025-06-07 01:36:40 UTC; unix
