Immune Deconvolution

Immune deconvolution is available through MCP counter, starting from an expression matrix tmm with samples as rows and genes as columns.

from tapir.immune import mcpc_estimate

estimates = mcpc_estimate(tmm)

For details on the deconvolution process, please see the MCPcounter publication [Becht2016].

References

Becht2016

Becht E., Giraldo N. A., Lacroix L., Buttard B., Elarouci N., Petitprez F., Selves J., Laurent-Puig P., Sautès-Fridman C., Fridman W. H. and de Reyniès A., (2016). “Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression”, Genome Biol. 20; 17(1) 218.