Package: rliger
Version: 2.2.1
Date: 2025-08-26
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
LinkingTo: Rcpp, RcppArmadillo, RcppProgress
Depends: methods, stats, utils, R (>= 3.5)
Imports: cli, DelayedArray, dplyr, ggplot2, grid, HDF5Array, hdf5r,
        leidenAlg (>= 1.1.1), lifecycle, magrittr, Matrix, RANN, Rcpp,
        RcppPlanc (>= 2.0.0), rlang, S4Vectors, scales, uwot
Suggests: AnnotationDbi, circlize, ComplexHeatmap, cowplot, DESeq2,
        EnhancedVolcano, fgsea, GenomicRanges, ggrepel, gprofiler2,
        IRanges, knitr, org.Hs.eg.db, plotly, psych, reactome.db,
        rmarkdown, Rtsne, sankey, scattermore (>= 0.7), Seurat,
        SeuratObject, SingleCellExperiment, SummarizedExperiment,
        testthat, viridis
NeedsCompilation: yes
Packaged: 2025-08-26 17:18:06 UTC; wangych
Repository: CRAN
Date/Publication: 2025-08-26 17:50:02 UTC
Built: R 4.5.3; x86_64-w64-mingw32; 2026-08-10 05:17:25 UTC; windows
Archs: x64
