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>.
README
# jrSiCKLSNMF
This package contains code to run joint graph-regularized single-cell Kullback-Leibler Non-negative Matrix Factorization
To install:
```{r package}
install.packages("devtools")
devtools::install_github("ellisdoro/jrSiCKLSNMF")
```
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Versions across snapshots
| Version | Repository | File | Size |
|---|---|---|---|
1.2.3 |
rolling linux/jammy R-4.5 | jrSiCKLSNMF_1.2.3.tar.gz |
928.7 KiB |
1.2.3 |
rolling linux/noble R-4.5 | jrSiCKLSNMF_1.2.3.tar.gz |
928.7 KiB |
1.2.3 |
rolling source/ R- | jrSiCKLSNMF_1.2.3.tar.gz |
928.7 KiB |
1.2.3 |
latest linux/jammy R-4.5 | jrSiCKLSNMF_1.2.3.tar.gz |
928.7 KiB |
1.2.3 |
latest linux/noble R-4.5 | jrSiCKLSNMF_1.2.3.tar.gz |
928.7 KiB |
1.2.3 |
latest source/ R- | jrSiCKLSNMF_1.2.3.tar.gz |
928.7 KiB |
1.2.3 |
2026-04-26 source/ R- | jrSiCKLSNMF_1.2.3.tar.gz |
928.7 KiB |
1.2.3 |
2026-04-23 source/ R- | jrSiCKLSNMF_1.2.3.tar.gz |
928.7 KiB |
1.2.2 |
2025-04-20 source/ R- | jrSiCKLSNMF_1.2.2.tar.gz |
928.7 KiB |