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: | 1.2.1 |
| 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 |
| LinkingTo: | Rcpp, RcppArmadillo, RcppProgress |
| Suggests: | knitr, rmarkdown |
| Published: | 2023-07-06 |
| 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 results |
Documentation:
| Reference manual: | jrSiCKLSNMF.pdf |
| Vignettes: |
Getting started with jrSiCKLSNMF Getting started with jrSiCKLSNMF with an L2 Norm Constraint on the columns of H Mini-batch jrSiCKLSNMF Tutorial |
Downloads:
| Package source: | jrSiCKLSNMF_1.2.1.tar.gz |
| Windows binaries: | r-devel: jrSiCKLSNMF_1.2.1.zip, r-release: jrSiCKLSNMF_1.2.1.zip, r-oldrel: jrSiCKLSNMF_1.2.1.zip |
| macOS binaries: | r-release (arm64): jrSiCKLSNMF_1.2.1.tgz, r-oldrel (arm64): jrSiCKLSNMF_1.2.1.tgz, r-release (x86_64): jrSiCKLSNMF_1.2.1.tgz, r-oldrel (x86_64): jrSiCKLSNMF_1.2.1.tgz |
Linking:
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