Package: monocle3
Title: Clustering, differential expression, and trajectory analysis for
        single- cell RNA-Seq
Version: 0.1.3
Authors@R: 
    person(given = "Hannah",
           family = "Pliner",
           role = c("aut", "cre"),
           email = "hpliner@uw.edu")
    person(given = "Xiaojie",
           family = "Qiu",
           role = c("aut", "cre"),
           email = "xqiu@uw.edu")
    person(given = "Cole",
           family = "Trapnell",
           role = c("aut", "cre"),
           email = "coletrap@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.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 6.1.1
LinkingTo: Rcpp
Depends: Biobase, SingleCellExperiment
Imports: assertthat (>= 0.2.1), BiocGenerics (>= 0.28.0), DelayedArray
        (>= 0.8.0), DelayedMatrixStats (>= 1.4.0), dplyr (>= 0.8.0.1),
        ggplot2 (>= 3.1.1), ggrepel (>= 0.8.1), grr, htmlwidgets (>=
        1.3), igraph (>= 1.2.4), irlba (>= 2.3.3), limma (>= 3.38.3),
        lmtest (>= 0.9-36), MASS (>= 7.3-51.4), Matrix (>= 1.2-17),
        Matrix.utils, methods, pbapply (>= 1.4-0), pbmcapply (>=
        1.4.1), pheatmap, plotly (>= 4.9.0), plyr (>= 1.8.4), proxy (>=
        0.4-23), pryr (>= 0.1.4), pscl (>= 1.5.2), purrr (>= 0.3.2),
        RANN (>= 2.6.1), Rcpp (>= 1.0.1), RcppParallel, reshape2 (>=
        1.4.3), reticulate (>= 1.11.1), rsample (>= 0.0.5),
        RhpcBLASctl, Rtsne (>= 0.15), S4Vectors, shiny, slam (>=
        0.1-45), spdep (>= 1.1-2), speedglm (>= 0.3-2), stringr (>=
        1.4.0), SummarizedExperiment (>= 1.11.5), uwot (>= 0.1.3),
        tibble (>= 2.1.1), tidyr (>= 0.8.3), viridis (>= 0.5.1)
Suggests: testthat (>= 2.1.0), ggrastr, knitr, rmarkdown, spelling
VignetteBuilder: knitr
Language: en-US
Remotes: VPetukhov/ggrastr
Author: Cole Trapnell [aut, cre]
Maintainer: Cole Trapnell <coletrap@uw.edu>
Built: R 3.6.1; x86_64-conda_cos6-linux-gnu; 2019-09-12 14:36:20 UTC; unix
