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) , and Liu J, Gao C, Sodicoff J, et al (2020) for more details.


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install.packages("rliger")

1.0.0 by Chao Gao, 5 months ago


https://github.com/welch-lab/liger


Report a bug at https://github.com/welch-lab/liger/issues


Browse source code at https://github.com/cran/rliger


Authors: Joshua Welch [aut, ctb] , Chao Gao [aut, ctb, cre] , Jialin Liu [aut, ctb] , Joshua Sodicoff [aut, ctb] , Velina Kozareva [aut, ctb] , Evan Macosko [aut, ctb] , Paul Hoffman [ctb] , Ilya Korsunsky [ctb] , Robert Lee [ctb]


Documentation:   PDF Manual  


GPL-3 license


Imports Rcpp, plyr, FNN, dplyr, grid, ggrepel, irlba, ica, Rtsne, ggplot2, riverplot, foreach, parallel, doParallel, mclust, stats, psych, RANN, uwot, rlang, utils, hdf5r

Depends on cowplot, Matrix, methods, patchwork

Suggests Seurat, knitr, reticulate, rmarkdown, testthat, GenomicRanges, S4Vectors, IRanges, org.Hs.eg.db, reactome.db, fgsea, AnnotationDbi

Linking to Rcpp, RcppArmadillo, RcppEigen, RcppProgress


See at CRAN