https://github.com/bioconductor-source/tbsignatureprofiler
Science Score: 26.0%
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○CITATION.cff file
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✓codemeta.json file
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○.zenodo.json file
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Found 1 DOI reference(s) in README -
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○Scientific vocabulary similarity
Low similarity (14.6%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: bioconductor-source
- License: other
- Language: R
- Default Branch: devel
- Size: 15.2 MB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
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:
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()
Owner
- Name: (WIP DEV) Bioconductor Packages
- Login: bioconductor-source
- Kind: organization
- Email: maintainer@bioconductor.org
- Website: https://bioconductor.org
- Repositories: 1
- Profile: https://github.com/bioconductor-source
Source code for packages accepted into Bioconductor
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Dependencies
- R >= 4.2.0 depends
- ASSIGN >= 1.23.1 imports
- BiocParallel * imports
- ComplexHeatmap * imports
- DESeq2 * imports
- DT * imports
- GSVA >= 1.51.3 imports
- RColorBrewer * imports
- ROCit * imports
- S4Vectors * imports
- SummarizedExperiment * imports
- edgeR * imports
- gdata * imports
- ggplot2 * imports
- magrittr * imports
- methods * imports
- reshape2 * imports
- rlang * imports
- singscore * imports
- stats * imports
- BiocStyle * suggests
- HGNChelper * suggests
- MASS * suggests
- caret * suggests
- circlize * suggests
- class * suggests
- covr * suggests
- dplyr * suggests
- e1071 * suggests
- glmnet * suggests
- impute * suggests
- knitr * suggests
- lintr * suggests
- pROC * suggests
- plyr * suggests
- randomForest * suggests
- rmarkdown * suggests
- shiny * suggests
- spelling * suggests
- sva * suggests
- testthat * suggests