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: |
1.0.1 |
Depends: |
R (≥ 3.4), Matrix, methods, stats, utils |
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 |
LinkingTo: |
Rcpp, RcppArmadillo, RcppEigen, RcppProgress |
Suggests: |
Seurat, SeuratObject, knitr, reticulate, rmarkdown, testthat, GenomicRanges, S4Vectors, IRanges, org.Hs.eg.db, reactome.db, fgsea, AnnotationDbi |
Published: |
2023-11-08 |
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 at umich.edu> |
BugReports: |
https://github.com/welch-lab/liger/issues |
License: |
GPL-3 |
URL: |
https://github.com/welch-lab/liger |
NeedsCompilation: |
yes |
Materials: |
README NEWS |
CRAN checks: |
rliger results |