tdw1221/NITUMID: Non-negative Matrix Factorization-based Immune-TUmor MIcroenvironment Deconvolution

NITUMID (Non-negative Matrix Factorization-based Immune-TUmor MIcroenvironment Deconvolution framework) is a package for tumor-immmune microenvironment profiling via gene expression data. It takes advantage of non-negative matrix factorization (NMF) to simultaneously give estimates of both each component cell type's signature genes' expression (mRNA) levels, as well as their proportions in the mixture. It takes an ordinary gene expression matrix as input, and outputs signature genes' levels as well as cell types' proportions. Also, you could choose to input your own siganture genes.

Getting started

Package details

AuthorDaiwei Tang, Seyoung Park
MaintainerThe package maintainer <[email protected]>
LicenseGPL-2
Version0.1.0
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("devtools")
library(devtools)
install_github("tdw1221/NITUMID")
tdw1221/NITUMID documentation built on Jan. 17, 2019, 12:46 a.m.