README.md

In dfjenkins3/TBSignatureProfiler: Profile RNA-Seq Data Using TB Pathway Signatures

TBSignatureProfiler

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 https://wejlab.github.io/TBSignatureProfiler-docs/.

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:

if (!requireNamespace("devtools", quietly = TRUE))
  install.packages("devtools")
devtools::install_github("wejlab/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!

library(TBSignatureProfiler)
TBSPapp()

dfjenkins3/TBSignatureProfiler documentation built on April 6, 2024, 2:38 p.m.