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: 2.0.1
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: 2024-04-04
DOI: NA
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

Documentation:

Reference manual: rliger.pdf
Vignettes: Data Integration with LIGER

Downloads:

Package source: rliger_2.0.1.tar.gz
Windows binaries: r-devel: rliger_2.0.1.zip, r-release: rliger_2.0.1.zip, r-oldrel: rliger_2.0.1.zip
macOS binaries: r-release (arm64): rliger_2.0.1.tgz, r-oldrel (arm64): rliger_2.0.1.tgz, r-release (x86_64): rliger_2.0.1.tgz, r-oldrel (x86_64): rliger_2.0.1.tgz
Old sources: rliger archive

Reverse dependencies:

Reverse suggests: scCustomize

Linking:

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