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: 1.0.0
Depends: cowplot, Matrix, methods, patchwork
Imports: Rcpp (≥ 0.12.10), plyr, FNN, dplyr, grid, ggrepel, irlba, ica, Rtsne, ggplot2, riverplot, foreach, parallel, doParallel, mclust, stats, psych, RANN, uwot, rlang, utils, hdf5r
LinkingTo: Rcpp, RcppArmadillo, RcppEigen, RcppProgress
Suggests: Seurat, knitr, reticulate, rmarkdown, testthat, GenomicRanges, S4Vectors, IRanges, org.Hs.eg.db, reactome.db, fgsea, AnnotationDbi
Published: 2021-04-19
Author: 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]
Maintainer: Chao Gao <gchao at umich.edu>
BugReports: https://github.com/welch-lab/liger/issues
License: GPL-3
URL: https://github.com/welch-lab/liger
NeedsCompilation: yes
Materials: README
CRAN checks: rliger results

Documentation:

Reference manual: rliger.pdf

Downloads:

Package source: rliger_1.0.0.tar.gz
Windows binaries: r-devel: rliger_1.0.0.zip, r-devel-UCRT: rliger_1.0.0.zip, r-release: rliger_1.0.0.zip, r-oldrel: rliger_1.0.0.zip
macOS binaries: r-release (arm64): rliger_1.0.0.tgz, r-release (x86_64): rliger_1.0.0.tgz, r-oldrel: rliger_1.0.0.tgz
Old sources: rliger archive

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