CRAN/E | rliger

rliger

Linked Inference of Genomic Experimental Relationships

Installation

About

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.

welch-lab.github.io/liger/
Bug report File report

Key Metrics

Version 2.0.1
R ≥ 3.5
Published 2024-04-04 15 days ago
Needs compilation? yes
License GPL-3
CRAN checks rliger results

Downloads

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Maintainer

Maintainer

Yichen Wang

wayichen@umich.edu

Authors

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

Material

README
NEWS
Reference manual
Package source

Additional repos

welch-lab.r-universe.dev
blaserlab.r-universe.dev

Vignettes

Data Integration with LIGER

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

rliger archive

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

Suggests

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DESeq2
DoubletFinder ≥ 2.0.4
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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

LinkingTo

Rcpp
RcppArmadillo
RcppProgress

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