Skip to content


Switch branches/tags

Name already in use

A tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. Are you sure you want to create this branch?

Latest commit


Git stats


Failed to load latest commit information.
Latest commit message
Commit time


tReasure (tRNA Expression Analysis Software Utilizing R for Easy use) is user-friendly tool for the tRNA expression analysis of deep-sequencing experiments for small RNAs using R packages.

tReasure currently implements the following tasks:
1) Making sample list for analysis
2) Pre-processing of trimming adapter and filtering reads
3) Alignment and quantification
4) Statistical analysis for differentially expressed tRNAs gene
5) Visualization 

🌱 Installation

tReasure is a package for the R computing environment and it is assumed that you have already installed R according to your operating system. See the R project at ( tReasure requires the gwidget2 graphical library to run and a few additional packages for the analysis of RNA-seq.

πŸ”” Notics

  • tReasure works fine with version R4.1. After being updated to the latest R version 4.2, an error has been identified in the tReasure. As soon as possible, we will revise the code and announce it again.
  • Being tested using conda as an alternative to install.
    • 2022-11-02 completion: under R4.1 using conda on Ubuntu.
    • 2022-11-02 ongoing: under R4.1 using conda on Mac

1. Preliminaries

  1. For window users :
    User need to install Rtools before installing tReasure.

  2. For linux users :
    Users need to install libcurl4-openssl-dev and libssl-dev for devtools.

    • Example for user Ubuntu
    sudo apt-get install libcurl4-openssl-dev 
    sudo apt-get install libssl-dev

    Also, user need to install libgtk2.0-dev and libxml2-dev for tReasure.

    • Example for user Ubuntu
    sudo apt-get update -y
    sudo apt-get install -y libxml2-dev
    sudo apt-get install -y libgtk2.0-dev
  3. For Mac OS users :
    Users need to install opnssl for devtools.

    • Example using brew
    brew update
    brew install openssl

    Users need to install XQuartz, gtk2 and cairo before installing tReasure.

    • Example using brew
    brew install cairo  
    brew install gtk+

2. Installation of tReasure : Open Rstudio or R and type as below.

It takes a few minutes to install for the first time.


 devtools::install_github("jinoklee/tReasure",force = TRUE)

Note If the descriptioin shows as below during the installation, choose "Install GTK+"

Need GTK+? (Restart Required)
    Install GTK+
    Do not install GTK+

Note If the installation was successful, the tReasure window appears. If the window dose not appear, restart R and type as below.


🌱 Installation using conda

  1. For Ubuntu :
  • Install miniconda and create enviroment
    conda create --name r4.1
    conda activate r4.1
  • Install Mamba for bioinformatics packages in conda and need to update conda.
    conda install mamba -c conda-forge -y
    conda update conda -y
    conda update -all 
  • Install R 4.1 and required packages.
    mamba install -c conda-forge r-base=4.1.2
    mamba install -c conda-forge r-devtools
    mamba install -c conda-forge r-rgtk2
    mamba install -c conda-forge r-cairodevice
  • Open R and type as below
    devtools::install_github("jinoklee/tReasure",force = TRUE)

🌱 Running tReasure

Open Rstuido or R and type as below


πŸ”” User Manual

πŸ”” Detailed Mapping Methods

πŸ”” Indiced reference

  • tReasure is automatically downloaded during analysis. If an error occurs during download, we recommend that you download the file directly, and then move it to a specific location, and unzip it.
    • Make folder (Hsapi38 or Mmusc10) on tReasure package folder. ex) [R4.1 PATH]/library/tReasure/extdata/refer/Hsapi38/
    • Move and extract the downloaded files into the folder created.
    • Homo sapiens hg38
    • Mus musculus 10

πŸ”” Sample Data

  • Small RNA-seq dataset from human breast tissues (part of GSE68085)
    • Download
    • Control (Normal): SRR1982473, SRR1982474, SRR1982475
    • Test (Cancer): SRR1982580, SRR1982581, SRR1982582

πŸ”” Tutorial Videos


No description, website, or topics provided.







No packages published