TransTEx (Transcript-level Tissue Expression)

TransTEx is a comprehensive R package developed by the Davuluri Lab for analyzing and exploring tissue-specific transcript/gene expression patterns. This tool introduces a novel tissue-specificity scoring method to group the human transcriptome into distinct expression categories. TransTEx enables the discovery of tissue-specific and tissue-enhanced transcripts across conditions using bulk-transcriptomic data.

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🔗 Important Links

• 📄 Published Paper
• 🌐 Online Database Note: The database may work best on either LTE or Wi-Fi — try switching networks if it doesn’t load.
• 🎥 Introductory Talk

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📦 Installation

Before installing TransTEx, make sure R is installed on your system. Then install required dependencies and the package itself:

install.packages("remotes")
BiocManager::install("edgeR")
remotes::install_github("pallavisurana1/TransTEx")

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🚀 Getting Started

Load the package in R:

library(TransTEx)

Explore available functions and documentation:

help(package = "TransTEx")

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📘 Usage Examples

Access detailed usage examples and workflows via the package vignettes:

browseVignettes("TransTEx")

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🛠 Reporting Issues

Found a bug or issue? Report it on the official GitHub repository:

👉 GitHub Issues

We welcome community feedback and contributions!

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📖 Citation

If you use TransTEx in your work, please cite the following:

@article{Surana2024,
  author    = {Pallavi Surana and Pratik Dutta and Ramana V Davuluri},
  title     = {TransTEx: novel tissue-specificity scoring method for grouping human transcriptome into different expression groups},
  journal   = {Bioinformatics},
  volume    = {40},
  number    = {8},
  year      = {2024},
  article   = {btae475},
  doi       = {10.1093/bioinformatics/btae475},
  url       = {https://doi.org/10.1093/bioinformatics/btae475}
}

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📬 Contact

For inquiries or more information about TransTEx, please contact: Pallavi Surana 📧 pallavi.surana@stonybrook.edu

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📄 License

TransTEx is made available under the MIT License. Please see the LICENSE file for details.