https://github.com/wejlab/tbsignatureprofiler

Profile RNA-seq data using published TB gene signatures
https://github.com/wejlab/tbsignatureprofiler

bioconductor-package biomarkers gene-signatures tuberculosis

Last synced: 3 months ago
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Profile RNA-seq data using published TB gene signatures

• Host: GitHub
• URL: https://github.com/wejlab/tbsignatureprofiler
• Owner: wejlab
• License: other
• Created: 2018-08-30T16:19:47.000Z (almost 8 years ago)
• Default Branch: devel
• Last Pushed: 2025-09-24T14:58:10.000Z (9 months ago)
• Last Synced: 2025-09-24T16:42:04.477Z (9 months ago)
• Topics: bioconductor-package, biomarkers, gene-signatures, tuberculosis
• Language: R
• Homepage:
• Size: 15.6 MB
• Stars: 12
• Watchers: 2
• Forks: 13
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: NEWS.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md

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README

          
## TBSignatureProfiler 

[![](https://img.shields.io/badge/bioconductor-3.21-blue)](http://www.bioconductor.org/packages/release/bioc/html/TBSignatureProfiler.html)

[![codecov](https://codecov.io/gh/wejlab/TBSignatureProfiler/branch/master/graph/badge.svg)](https://codecov.io/gh/wejlab/TBSignatureProfiler)

[![build](http://www.bioconductor.org/shields/build/devel/bioc/TBSignatureProfiler.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/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”](

https://bmcinfectdis.biomedcentral.com/articles/10.1186/s12879-020-05598-z)

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()

```