Package: rliger
Version: 1.0.0
Date: 2021-03-09
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', 'ctb')),
  person(given = 'Chao', family = 'Gao', email = 'gchao@umich.edu', role = c('aut', 'ctb', 'cre')),
  person(given = 'Jialin', family = 'Liu', email = 'alanliu@umich.edu', role = c('aut', 'ctb')),
  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')
  )
Author: Joshua Welch [aut, ctb], 
        Chao Gao [aut, ctb, cre], 
        Jialin Liu [aut, ctb], 
        Joshua Sodicoff [aut, ctb],
        Velina Kozareva [aut, ctb],
        Evan Macosko [aut, ctb],
        Paul Hoffman [ctb],
        Ilya Korsunsky [ctb],
        Robert Lee [ctb]
Maintainer: Chao Gao <gchao@umich.edu>
BugReports: https://github.com/welch-lab/liger/issues
URL: https://github.com/welch-lab/liger
License: GPL-3 | file LICENSE
Imports: Rcpp (>= 0.12.10),
     plyr,
     FNN,
     dplyr,
     grid,
     ggrepel,
     irlba,
     ica,
     Rtsne,
     ggplot2,
     riverplot,
     foreach,
     parallel,
     doParallel,
     mclust,
     stats,
     psych,
     RANN,
     uwot,
     rlang,
     utils,
     hdf5r,
     scattermore (>= 0.7)
biocViews:
LazyData: true
LinkingTo: Rcpp, RcppArmadillo, RcppEigen, RcppProgress
Depends:
    cowplot,
    Matrix,
    methods,
    patchwork
RoxygenNote: 7.1.1
Encoding: UTF-8
Suggests:
    Seurat,
    knitr,
    reticulate,
    rmarkdown,
    testthat,
    GenomicRanges,
    S4Vectors,
    IRanges,
    org.Hs.eg.db,
    reactome.db,
    fgsea,
    AnnotationDbi
VignetteBuilder: knitr