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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: | 2.1.0 |
| Depends: | methods, stats, utils, R (≥ 3.5) |
| Imports: | circlize, cli, cowplot, ComplexHeatmap, dplyr, ggplot2, grid, hdf5r, leidenAlg (≥ 1.1.1), lifecycle, magrittr, Matrix, RANN, RColorBrewer, Rcpp, rlang, Rtsne, S4Vectors, scales, uwot, viridis |
| LinkingTo: | Rcpp, RcppArmadillo, RcppProgress |
| Suggests: | AnnotationDbi, DESeq2, DoubletFinder (≥ 2.0.4), EnhancedVolcano, fgsea, GenomicRanges, ggrepel, gprofiler2, IRanges, knitr, org.Hs.eg.db, plotly, psych, RcppPlanc, reactome.db, rmarkdown, sankey, scattermore (≥ 0.7), Seurat, SeuratObject, SingleCellExperiment, SummarizedExperiment, testthat |
| Published: | 2024-10-29 |
| 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 |
| Additional_repositories: | https://welch-lab.r-universe.dev, https://blaserlab.r-universe.dev |
| Materials: | README NEWS |
| CRAN checks: | rliger results |
| Reference manual: | rliger.pdf |
| Vignettes: |
Data integration with LIGER (source, R code) |
| Package source: | rliger_2.1.0.tar.gz |
| Windows binaries: | r-devel: rliger_2.1.0.zip, r-release: rliger_2.1.0.zip, r-oldrel: rliger_2.1.0.zip |
| macOS binaries: | r-release (arm64): rliger_2.1.0.tgz, r-oldrel (arm64): rliger_2.1.0.tgz, r-release (x86_64): rliger_2.1.0.tgz, r-oldrel (x86_64): rliger_2.1.0.tgz |
| Old sources: | rliger archive |
| Reverse suggests: | scCustomize |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.