The goal of quantiseqr is to streamline the quantification of tumor immune contexture from RNA-seq data using quanTIseq.
quanTIseq is deconvolution method based on an RNA-seq-derived signature matrix (i.e., TIL10) designed and validated to quantify 10 different immune cell types.
Please see (Finotello F et al., Genome Medicine 2019) for additional details on quanTIseq.
You can install the development version of quantiseqr from GitHub with:
library("remotes")
remotes::install_github("federicomarini/quantiseqr",
dependencies = TRUE, build_vignettes = TRUE)You can find the rendered version of the documentation of quantiseqr at the project website https://federicomarini.github.io/quantiseqr, created with pkgdown.
If you encounter a bug, have usage questions, or want to share ideas and functionality to make this package better, feel free to file an issue.
Please note that the quantiseqr project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
If you use this package in your work, please cite the original quanTIseq study:
Finotello F, Mayer C, Plattner C, Laschober G, Rieder D, Hackl H, Krogsdam A, Loncova Z, Posch W, Wilflingseder D, Sopper S, Ijsselsteijn M, Brouwer TP, Johnson D, Xu Y, Wang Y, Sanders ME, Estrada MV, Ericsson-Gonzalez P, Charoentong P, Balko J, de Miranda NFDCC, Trajanoski Z. Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data. Genome Medicine, 2019. 11(1):34. https://doi.org/10.1186/s13073-019-0638-6