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.
| Version: |
2.2.1 |
| 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 |
| LinkingTo: |
Rcpp, RcppArmadillo, RcppProgress |
| 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 |
| Published: |
2025-08-26 |
| DOI: |
10.32614/CRAN.package.rliger |
| 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 at umich.edu> |
| BugReports: |
https://github.com/welch-lab/liger/issues |
| License: |
GPL-3 |
| URL: |
https://welch-lab.github.io/liger/ |
| NeedsCompilation: |
yes |
| Materials: |
README, NEWS |
| CRAN checks: |
rliger results |