tme_deconvolution_methods: TME Deconvolution Methods

In IOBR: Immune Oncology Biological Research

TME Deconvolution Methods

Description

A named vector of supported tumor microenvironment (TME) deconvolution methods in the IOBR package.

Usage

tme_deconvolution_methods

Format

A named character vector where names are display names and values are internal method names.

Details

The methods currently supported are:

• 'mcpcounter': MCP-counter for immune and stromal cell populations

• 'epic': EPIC for immune, stromal, and cancer cell fractions

• 'xcell': xCell for 64 immune and stromal cell types

• 'cibersort': CIBERSORT for 22 immune cell types

• 'cibersort_abs': CIBERSORT in absolute mode

• 'ips': Immunophenoscore calculation

• 'estimate': ESTIMATE for stromal/immune/estimate scores

• 'svr': Support Vector Regression (custom reference)

• 'lsei': Least Squares with Equality/Inequality constraints

• 'timer': TIMER for cancer-specific immune estimation

• 'quantiseq': quanTIseq for RNA-seq immune deconvolution

Value

Named character vector of available deconvolution methods.

Examples

# List all available TME deconvolution methods
tme_deconvolution_methods

# Get internal method name for a specific method
tme_deconvolution_methods["MCPcounter"]

IOBR documentation built on May 30, 2026, 5:07 p.m.