The TBSignatureProfiler (TBSP) is an easy-to-use R package for analysis of RNA-seq data using gene signatures for tuberculosis disease presence, risk, progression, treatment failure, and other states. In-package signature profiling is available using common gene set enrichment tools that include GSVA, singscore, and ssGSEA.
Users can compare RNA-seq data across 70+ published gene signatures to compare signature performance with clear visualizations (e.g., heatmaps and ROC plots), specificity/sensitivity estimates for predicting binary variables, and cross-validated logistic regression.
The TBSP can be used as a standalone software package. Data exploration is also available with the accompanying interactive R Shiny application. The R Shiny app is currently functional but more limited in its capabilities than the command line form of the package.
We used the TBSP to compare 45 gene signatures and differentiate active TB from LTBI in malnourished individuals from India. You can read our paper here: “Comparing tuberculosis gene signatures in malnourished individuals using the TBSignatureProfiler”
Johnson, W.E., Odom, A., Cintron, C. et al. Comparing tuberculosis gene signatures in malnourished individuals using the TBSignatureProfiler. BMC Infect Dis 21, 106 (2021).
Check the “Tutorials” tab at the top of the page for guided walkthroughs of how to run the TBSP and compare gene signatures. “Command Line Analysis” is the best place to begin.
The TBSignatureProfiler requires R Version 4.1.
- Install the development version of the package from Github:
if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools") devtools::install_github("compbiomed/TBSignatureProfiler")
- Install the release version of the package from Bioconductor:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("TBSignatureProfiler")
- Run the TBSP R Shiny app!