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## TBSignatureProfiler <img src="" align="right" width="170" /> [![](]( [![codecov](]( [![build](]( ## What is the TBSignatureProfiler? 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 analyze 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. ## Documentation Please check our website at ## Citation 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”]( Please cite: **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).** ## Installation The TBSignatureProfiler requires R Version 4.2. * Install the development version of the package from Github: ``` r if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools") devtools::install_github("wejlab/TBSignatureProfiler") ``` * Install the release version of the package from Bioconductor: ``` r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("TBSignatureProfiler") ``` * Run the TBSP R Shiny app! ``` r library(TBSignatureProfiler) TBSPapp() ```