Package: rliger
Version: 1.0.1
Date: 2023-11-08
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')),
  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 = 'Yichen', family = 'Wang', email = 'wayichen@umich.edu', role = c('aut', 'ctb', 'cre')),
  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],
  Jialin Liu [aut, ctb],
  Joshua Sodicoff [aut, ctb],
  Velina Kozareva [aut, ctb],
  Evan Macosko [aut, ctb],
  Yichen Wang [aut, ctb, cre],
  Paul Hoffman [ctb],
  Ilya Korsunsky [ctb],
  Robert Lee [ctb]
Maintainer: Yichen Wang <wayichen@umich.edu>
BugReports: https://github.com/welch-lab/liger/issues
URL: https://github.com/welch-lab/liger
License: GPL-3
Imports: Rcpp (>= 0.12.10), plyr, FNN, dplyr, grid, ggrepel, irlba,
        ica, Rtsne, ggplot2, foreach, parallel, doParallel, mclust,
        psych, RANN, uwot, rlang, hdf5r, scattermore (>= 0.7),
        patchwork, cowplot
biocViews:
LazyData: true
LinkingTo: Rcpp, RcppArmadillo, RcppEigen, RcppProgress
Depends: R (>= 3.4), Matrix, methods, stats, utils
RoxygenNote: 7.2.3
Encoding: UTF-8
Suggests: Seurat, SeuratObject, knitr, reticulate, rmarkdown, testthat,
        GenomicRanges, S4Vectors, IRanges, org.Hs.eg.db, reactome.db,
        fgsea, AnnotationDbi
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2023-11-08 18:55:20 UTC; wangych
Repository: CRAN
Date/Publication: 2023-11-08 23:30:02 UTC
Built: R 4.2.0; x86_64-apple-darwin17.0; 2023-12-21 20:40:33 UTC; unix
Archs: rliger.so.dSYM
