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DeMixT (v 1.10.1)

DeMixT is a frequentist-based method and fast in yielding accurate estimates of cell proportions and compartment-specific expression profiles for two- and three-component deconvolution from heterogeneous tumor samples.

Installation

The DeMixT source files are compatible with Windows, Linux and MacOS.

This version is for users who have OpenMP on the computer. We recommend the user to install DeMixT (v 1.10.0) from Bioconductor:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DeMixT")

If needed, the user can install the latest DeMixT (v 1.10.1) from GitHub:

if (!require("devtools", quietly = TRUE))
    install.packages('devtools')

devtools::install_github("wwylab/DeMixT")

Check if DeMixT is installed successfully:

# load package
library(DeMixT)

Use DeMixT

A tutorial is available at https://wwylab.github.io/DeMixT/.

Cite DeMixT

[1] Ahn, J. et al. DeMix: Deconvolution for mixed cancer transcriptomes using raw measured data. Bioinformatics 29, 1865–1871 (2013).

[2] Wang, Z. et al. Transcriptome Deconvolution of Heterogeneous Tumor Samples with Immune Infiltration. iScience 9, 451–460 (2018).