DESCRIPTION

Package: rliger
Version: 2.1.0.9003
Date: 2024-12-04
Type: Package
Title: Linked Inference of Genomic Experimental Relationships
Description: Uses an extension of nonnegative matrix factorization to identify shared and dataset-specific factors. See Welch J, Kozareva V, et al (2019) <doi:10.1016/j.cell.2019.05.006>, and Liu J, Gao C, Sodicoff J, et al (2020) <doi:10.1038/s41596-020-0391-8> for more details.
Authors@R: c(
  person(given = 'Joshua', family = 'Welch', email = 'welchjd@umich.edu', role = c('aut')),
  person(given = 'Yichen', family = 'Wang', email = 'wayichen@umich.edu', role = c('aut', 'cre')),
  person(given = 'Chao', family = 'Gao', email = 'gchao@umich.edu', role = c('aut')),
  person(given = 'Jialin', family = 'Liu', email = 'alanliu@umich.edu', role = c('aut')),
  person(given = 'Joshua', family = 'Sodicoff', email = 'sodicoff@umich.edu', role = c('aut', 'ctb')),
  person(given = 'Velina', family = 'Kozareva', role = c('aut', 'ctb')),
  person(given = 'Evan', family = 'Macosko', role = c('aut', 'ctb')),
  person(given = 'Paul', family = 'Hoffman', role = 'ctb'),
  person(given = 'Ilya', family = 'Korsunsky', role = 'ctb'),
  person(given = 'Robert', family = 'Lee', role = 'ctb'),
  person(given = 'Andrew', family = 'Robbins', email = 'robbiand@med.umich.edu', role = 'ctb')
  )
Author: Joshua Welch [aut],
        Yichen Wang [aut, cre],
        Chao Gao [aut],
        Jialin Liu [aut],
        Joshua Sodicoff [aut, ctb],
        Velina Kozareva [aut, ctb],
        Evan Macosko [aut, ctb],
        Paul Hoffman [ctb],
        Ilya Korsunsky [ctb],
        Robert Lee [ctb],
        Andrew Robbins [ctb]
Maintainer: Yichen Wang <wayichen@umich.edu>
BugReports: https://github.com/welch-lab/liger/issues
URL: https://welch-lab.github.io/liger/
License: GPL-3
biocViews:
LazyData: true
RoxygenNote: 7.3.2
VignetteBuilder: knitr
Encoding: UTF-8
Additional_repositories: https://welch-lab.r-universe.dev, https://blaserlab.r-universe.dev
LinkingTo: Rcpp, RcppArmadillo, RcppProgress
Depends:
    methods,
    stats,
    utils,
    R (>= 3.5)
Imports:
    circlize,
    cli,
    cowplot,
    ComplexHeatmap,
    dplyr,
    ggplot2,
    grid,
    hdf5r,
    leidenAlg (>= 1.1.1),
    lifecycle,
    magrittr,
    Matrix,
    RANN,
    RColorBrewer,
    Rcpp,
    rlang,
    Rtsne,
    S4Vectors,
    scales,
    uwot,
    viridis
Suggests:
    AnnotationDbi,
    DESeq2,
    DoubletFinder (>= 2.0.4),
    EnhancedVolcano,
    fgsea,
    GenomicRanges,
    ggrepel,
    gprofiler2,
    IRanges,
    knitr,
    org.Hs.eg.db,
    plotly,
    psych,
    RcppPlanc,
    reactome.db,
    rmarkdown,
    sankey,
    scattermore (>= 0.7),
    Seurat,
    SeuratObject,
    SingleCellExperiment,
    SummarizedExperiment,
    testthat
Roxygen: list(markdown = TRUE)