Multimodal Single-Cell Omics Dimensionality Reduction
Overview
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.
- Adjusted dependency on scran to dependency on bluster and replaced the buildSNNGraph and buildKNNGraph functions from scran with the makeSNNGraph and makeKNNGraph functions from bluster
From NEWS.md in the release
Install
Health
ERRORpackage dependenciesr-oldrel-macos-arm64
Package required but not available: ‘bluster’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
- ERROR12 OK, 1 ERRORNow
- ERROR6 OK, 6 WARNING, 1 ERROR2026-05-16
- WARNING5 OK, 8 WARNING2026-05-10
- ERROR5 OK, 7 WARNING, 1 ERROR2026-05-03
- WARNING7 OK, 2 NOTE, 5 WARNING2026-04-22
- ERROR6 OK, 2 NOTE, 5 WARNING, 1 ERROR2026-04-18
Show 3 earlier changesHide 3 earlier changes
- WARNING9 OK, 2 NOTE, 3 WARNING2026-04-10
- ERROR9 OK, 2 NOTE, 2 WARNING, 1 ERROR2026-04-09
- NOTE12 OK, 2 NOTE2026-03-10
Documentation
- Help pages
- 20
- Examples that run
- 88%14 run in a plain check · 2 never run
- Exported functions with examples
- 94%
- Documented parameters
- not tracked
- Return-value docs
- not tracked
- Help pages citing references
- 60% with a bibliography file
Downloads
Dependencies
Installing jrSiCKLSNMF adds 130 packages (65 with compiled code, 121 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB. 1 more not on CRAN is not measured.
Code & Tests
Datasets
People & History
Package metadata
- First published
- 2023-07-06
- Total releases
- 4 / 3 yrs
- License
- GPL-3 OSI
- Minimum R
- ≥ 3.5.0
- Bundled data
- 188 KB / 2 files
- Download size
- 1.0 MB
Cite
Cite this package
Run in R for the authors' entry:
citation("jrSiCKLSNMF")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.3389/fgene.2023.1179439.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.