NMF tools for scRNA analysis

Question

[P]

New to scRNA analysis, any suggestions on the an easy to use NMF tool? Something in R or python would be great! Thanks!

[ATpoint]

Some details on what you plan to do would help. https://osca.bioconductor.org/ is always a good read for any single-cell analysis.

Answer 1

[Bogdan]

you can please take a look into LIGER algorithm : https://github.com/welch-lab/liger

an example is outlined in the publication : https://www.biorxiv.org/content/10.1101/2020.04.07.029546v1.full

Answer 2

[zdebruine]

Use the RcppML package from CRAN, the nmf function. You'll find it exceptionally fast and easy to use. Native support for R Matrix::dgCMatrix.