Contains functions to generate gene expression signature values from (1) an expression matrix and (2) a list of genes.
calculateBuffa calculates a hypoxia signature from Buffa et al (2010).[1]
calculateMitoscore calculates a hypoxia signature from Benej et al (submitted).[2]
calculateAvgZScore calculates one or more signatures for which a vector of genes is z-score transformed and then the mean is reported.
calculateSCN calculates a Small Cell Neuroendocrine phenotype score from Balanis et al. (2019). [3]
Please see the user manual for more information.
# Currently available as the development version on GitHub
install.packages("devtools")
devtools::install_github("spakowiczlab/tmesig")- Buffa, F. M., et al. "Large meta-analysis of multiple cancers reveals a common, compact and highly prognostic hypoxia metagene." British journal of cancer 102.2 (2010): 428-435.
- Benej, M., et al. "Oxygen demand driven tumor hypoxia – a new perspective on the genesis and treatment of hypoxia." submitted
- Balanis et al. "Pan-cancer Convergence to a Small-Cell Neuroendocrine Phenotype that Shares Susceptibilities with Hematological Malignancies" Cancer Cell (2019)