DESCRIPTION

Package: monocle3
Title: Clustering, Differential Expression, and Trajectory Analysis for
    Single-Cell RNA-Seq
Version: 1.3.7
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: 7.2.3
LinkingTo: 
    Rcpp
Depends:
	R (>= 4.0.0),
    Biobase, 
    SingleCellExperiment
Imports:
    assertthat (>= 0.2.1),
    batchelor,
    BiocGenerics (>= 0.28.0),
    BiocParallel,
    DelayedArray (>= 0.8.0),
    DelayedMatrixStats (>= 1.4.0),
    digest (>= 0.6.28),
    dplyr (>= 0.8.0.1),
    future (>= 1.23.0),
    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: 
    testthat (>= 2.1.0),
    pryr (>= 0.1.4),
    knitr,
    rmarkdown,
    spelling,
    scran
VignetteBuilder: knitr
Language: en-US
NeedsCompilation: yes
Packaged: 2022-05-10 17:21:53 UTC; brent
Maintainer: Brent Ewing <bge@uw.edu>