TransTEx (Transcript-level Tissue Expression)

Novel tissue-specificity scoring method for grouping human transcriptome into different expression groups

TransTEx is a comprehensive R package developed by the Davuluri Lab for analyzing and exploring tissue-specific transcript/gene expression patterns. The package facilitates the identification of tissue-specific and tissue-enhanced transcripts across various conditions, leveraging bulk-transcriptomic data to uncover insights into gene expression dynamics.

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Installation

Before installing TransTEx, ensure you have R installed on your system. TransTEx can be installed directly from GitHub using the remotes package. If you do not have remotes installed, you can install it using the following command:

install.packages("remotes")

With remotes installed, proceed to install TransTEx:

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

Quick Start

Load TransTEx into your R session:

library(TransTEx)

Explore the functions and datasets provided by TransTEx:

help(package = "TransTEx")

Usage Examples

For detailed examples of using TransTEx to analyze tissue-specific gene expression, please refer to the vignettes:

browseVignettes("TransTEx")

Reporting Issues

If you encounter any bugs or issues while using TransTEx, please report them on the Issues page of the GitHub repository. We appreciate your contributions to improving TransTEx.

Citation

If you use TransTEx in your research, please cite:

@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}
}

Contact

For additional information or inquiries about TransTEx, please contact Pallavi Surana (pallavi.surana@stonybrook.edu)

License

TransTEx is made available under the (specify license, e.g., MIT License). See the LICENSE file for more details.