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:	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

Documentation:

Reference manual:	rliger.html , rliger.pdf
Vignettes:	Data integration with LIGER (source, R code)

Downloads:

Package source:	rliger_2.2.1.tar.gz
Windows binaries:	r-devel: rliger_2.2.1.zip, r-release: rliger_2.2.1.zip, r-oldrel: rliger_2.2.1.zip
macOS binaries:	r-release (arm64): rliger_2.2.1.tgz, r-oldrel (arm64): rliger_2.2.1.tgz, r-release (x86_64): rliger_2.2.1.tgz, r-oldrel (x86_64): rliger_2.2.1.tgz
Old sources:	rliger archive

Reverse dependencies:

Reverse suggests:

scCustomize

Linking:

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