DESCRIPTION

Package: MAST
Type: Package
Title: Model-based Analysis of Single Cell Transcriptomics
Version: 1.27.1
Date: 2023-04-20
Authors@R: c(person("Andrew", "McDavid", email = "Andrew_McDavid@urmc.rochester.edu", role = c("aut", "cre")),
            person("Greg", "Finak", email="gfinak@fredhutch.org", role='aut'),
            person("Masanao", "Yajima", email="myajima@fredhutch.org", role='aut'))
VignetteBuilder: knitr
Imports:
    Biobase,
    BiocGenerics,
    S4Vectors,
    data.table,
    ggplot2,
    plyr,
    stringr,
    abind,
    methods,
    parallel,
    reshape2,
    stats,
    stats4,
    graphics,
    utils,
    SummarizedExperiment(>= 1.5.3),
    progress,
    Matrix
Depends:
    SingleCellExperiment (>= 1.2.0),
    R(>= 3.5)
Suggests:
    knitr,
    rmarkdown,
    testthat,
    lme4(>= 1.0),
    blme,
    roxygen2(> 6.0.0),
    numDeriv,
    car,
    gdata,
    lattice,
    GGally,
    GSEABase,
    NMF,
    TxDb.Hsapiens.UCSC.hg19.knownGene,
    rsvd,
    limma,
    RColorBrewer,
    BiocStyle,
    scater,
    DelayedArray,
    HDF5Array,
    zinbwave,
    dplyr
Description: Methods and models for handling zero-inflated single cell
    assay data.
License: GPL(>= 2)
Collate:
    'AllGenerics.R'
    'AllClasses.R'
    'CovFromBoots.R'
    'Fluidigm-methods.R'
    'GSEA-by-boot.R'
    'Hypothesis.R'
    'LmWrapper.R'
    'MAST-package.R'
    'MultidimensionalScaling.R'
    'RNASeqAssay-methods.R'
    'Readers.R'
    'SingleCellAssay-methods.R'
    'UtilityFunctions.R'
    'ZlmFit-bootstrap.R'
    'ZlmFit-logFC.R'
    'ZlmFit.R'
    'bayesglm.R'
    'convertMASTClassic.R'
    'ebayes-helpers.R'
    'filterEval.R'
    'helper-methods.R'
    'lmWrapper-bayesglm.R'
    'lmWrapper-glm.R'
    'lmWrapper-glmer.R'
    'lmWrapper-ridge.R'
    'lrtest.R'
    'predict.R'
    'stat_ell.R'
    'thresholdSCRNA.R'
    'zeroinf.R'
    'zlmHooks.R'
RoxygenNote: 7.2.3
LazyData: true
biocViews: GeneExpression, DifferentialExpression, GeneSetEnrichment,
    RNASeq, Transcriptomics, SingleCell
BugReports: https://github.com/RGLab/MAST/issues
URL: https://github.com/RGLab/MAST/
Encoding: UTF-8