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.201905006>, 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
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年08月26日
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>
NeedsCompilation:
yes
Documentation:
Downloads:
Reverse dependencies:
Linking:
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