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.


Reference manual

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1.0.0 by Chao Gao, 9 months ago

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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,, reactome.db, fgsea, AnnotationDbi

Linking to Rcpp, RcppArmadillo, RcppEigen, RcppProgress

See at CRAN