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 [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 resultsRetroSearch is an open source project built by @garambo | Open a GitHub Issue
Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo
HTML:
3.2
| Encoding:
UTF-8
| Version:
0.7.4