Package: rliger
Version: 1.0.0
Date: 2021-04-18
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
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
biocViews:
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
NeedsCompilation: yes
Packaged: 2021-04-19 16:03:11 UTC; gchao
Repository: CRAN
Date/Publication: 2021-04-19 22:00:12 UTC
Built: R 4.0.5; x86_64-w64-mingw32; 2022-04-18 06:05:50 UTC; windows
Archs: i386, x64
