NMF tools for scRNA analysis
New to scRNA analysis, any suggestions on the an easy to use NMF tool? Something in R or python would be great! Thanks!
• 3,497 views
•
link
updated
by
zdebruine •
•
written
by
P •
•
written
by
P •
2 answers
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
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.
• 0 views
•
link
written
by
zdebruine •
Log in to answer this question.
More posts like this
-
How to interpret NMF clustering results
written by grsyhhsb •
-
Differential gene expression analysis in Python
written by Leendert •
-
Somatic Structure Variation on exome-seq data - pipeline recommendations?
written by wiki97 •
-
How to predict new data using NMF classifier
written by a511512345
-
which matrix should NMF use in single cell RNA seq data to find diferential gene program?
written by hq.huang11.6 •
-
How to analyze scRNA-seq data to compare lncRNA and mRNA
written by Kedu •
-
SPANR result interpretation
written by nkausthu •
-
Any workshop in Europe related with advance genome biology and Perl (or R or python)
written by Lila M
-
Which New Bioinformatics Related Tool Would You Appreciate The Most?
written by Biomonika (Noolean)
-
Hidden Markov Models In Genomic Analysis
written by didymos
Some details on what you plan to do would help. https://osca.bioconductor.org/ is always a good read for any single-cell analysis.