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Description

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>.

jrSiCKLSNMF

This package contains code to run joint graph-regularized single-cell Kullback-Leibler Non-negative Matrix Factorization

To install:

install.packages("devtools")
devtools::install_github("ellisdoro/jrSiCKLSNMF")

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Metadata

Version

1.2.1

License

Unknown

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