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tReasure


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 (http://www.r-project.org). 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.

 install.packages("devtools")
 library("devtools")

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

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.

tReasure::tReasure()

🌱 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
    library("devtools") 
    devtools::install_github("jinoklee/tReasure",force = TRUE)
    library("tReasure")
    install.tReasure()
    

🌱 Running tReasure

Open Rstuido or R and type as below

 library("tReasure")
 tReasure::tReasure()

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

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