jrSiCKLSNMF: Multimodal Single-Cell Omics Dimensionality Reduction

Methods to perform Joint graph Regularized Single-Cell Kullback-Leibler Sparse Non-negative Matrix Factorization ('jrSiCKLSNMF', pronounced "junior sickles NMF") on quality controlled single-cell multimodal omics count data. 'jrSiCKLSNMF' specifically deals with dual-assay scRNA-seq and scATAC-seq data. This package contains functions to extract meaningful latent factors that are shared across omics modalities. These factors enable accurate cell-type clustering and facilitate visualizations. Methods for pre-processing, clustering, and mini-batch updates and other adaptations for larger datasets are also included. For further details on the methods used in this package please see Ellis, Roy, and Datta (2023) <doi:10.3389/fgene.2023.1179439>.

Version: 1.2.3
Depends: R (≥ 3.5.0)
Imports: Rcpp (≥ 1.0.9), igraph, umap, kknn, ggplot2, methods, stats, rlang, Matrix, data.table, parallel, pbapply, cluster, MASS, clValid, factoextra, foreach, irlba, scran, Rdpack, ggrepel
LinkingTo: Rcpp, RcppArmadillo, RcppProgress
Suggests: knitr, rmarkdown
Published: 2025-07-11
DOI: 10.32614/CRAN.package.jrSiCKLSNMF
Author: Dorothy Ellis ORCID iD [aut, cre], Susmita Datta [ths], Kenneth Perkins [ctb] (Util.h function author, http://programmingnotes.org/), Renaud Gaujoux [ctb] (Author of .nndsvd R adaptation)
Maintainer: Dorothy Ellis <ddemoreellis at gmail.com>
License: GPL-3
NeedsCompilation: yes
Citation: jrSiCKLSNMF citation info
Materials: README, NEWS
CRAN checks: jrSiCKLSNMF results

Documentation:

Reference manual: jrSiCKLSNMF.html , jrSiCKLSNMF.pdf
Vignettes: Getting started with jrSiCKLSNMF (source, R code)
Getting started with jrSiCKLSNMF with an L2 Norm Constraint on the columns of H (source, R code)
Mini-batch jrSiCKLSNMF Tutorial (source, R code)

Downloads:

Package source: jrSiCKLSNMF_1.2.3.tar.gz
Windows binaries: r-devel: jrSiCKLSNMF_1.2.3.zip, r-release: jrSiCKLSNMF_1.2.3.zip, r-oldrel: jrSiCKLSNMF_1.2.3.zip
macOS binaries: r-release (arm64): jrSiCKLSNMF_1.2.3.tgz, r-oldrel (arm64): jrSiCKLSNMF_1.2.3.tgz, r-release (x86_64): jrSiCKLSNMF_1.2.3.tgz, r-oldrel (x86_64): jrSiCKLSNMF_1.2.3.tgz
Old sources: jrSiCKLSNMF archive

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