README.md

In lanagarmire/NMFEM: Non-negative Matrix Factorization analysis and module generation for scRNA-Seq data

NMFEM

Generate protein-protein interaction network modules from selected genes, using spin-glass algorithm.

Installation

install.packages(c("dplyr", "ggplot2", "devtools", "igraph"))
source("https://bioconductor.org/biocLite.R")
biocLite(c("topGO", "org.Mm.eg.db", "limma", "DESeq2", "clusterProfiler", "org.Hs.eg.db"))
devtools::install_github('lanagarmire/NMFEM')

Documentation

Help for the main functions can be found at:

?nmf_subpopulation
?spinglass_procedure

Example Code

library(NMFEM)
subp <- nmf_subpopulation(toy)
res <- spinglass_procedure(fpkm, phe, leading_genes, mppi, 'mouse')

Tutorial

A simple tutorial can be found here.

lanagarmire/NMFEM documentation built on May 20, 2019, 7:34 p.m.