Ritmic, for RegulatIon of Tumor MIcroenvironment Composition is an R package to study the link between the gene expression in a tumor and the microenvironment composition.
The pipeline Ritmic is in 4 steps:
- Deconvolution of the bulk samples to obtain the cell type composition.
- Extraction of the cancer expression.
- Differential analysis of the gene expression in the cancer component.
- Analyze of the link between the gene expression in the cancer and the tumor composition.
This package allows to use the method. The package Ritmic_simu implements simulations to test it.
To use the package
install.packages("devtools")
devtools::install_github(https://github.com/bcm-uga/Ritmic.git)