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: |
1.0.0 |
| Depends: |
cowplot, Matrix, methods, patchwork |
| 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 |
| LinkingTo: |
Rcpp, RcppArmadillo, RcppEigen, RcppProgress |
| Suggests: |
Seurat, knitr, reticulate, rmarkdown, testthat, GenomicRanges, S4Vectors, IRanges, org.Hs.eg.db, reactome.db, fgsea, AnnotationDbi |
| Published: |
2021-04-19 |
| 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 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 |
| CRAN checks: |
rliger results |