rliger: Linked Inference of Genomic Experimental Relationships

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


Reference manual: rliger.pdf
Vignettes: Comparing and contrasting heterogeneous single cell profiles using liger


Package source: rliger_1.0.1.tar.gz
Windows binaries: r-devel: rliger_1.0.1.zip, r-release: rliger_1.0.1.zip, r-oldrel: rliger_1.0.1.zip
macOS binaries: r-release (arm64): rliger_1.0.1.tgz, r-oldrel (arm64): rliger_1.0.1.tgz, r-release (x86_64): rliger_1.0.1.tgz
Old sources: rliger archive

Reverse dependencies:

Reverse suggests: scCustomize


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