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 |