README.md

In jinoklee/tReasure: tReasure

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.

🔔 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.

5) 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
 ```

2) 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()

🔔 User Manual

• Download

🔔 Detailed Mapping Methods

• Click

🔔 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

🔔 Sample Data

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

🔔 Tutorial Videos

• Installation and setup: Window
• Full version of analysis: Window Mac
• Results folders: Click

jinoklee/tReasure documentation built on Nov. 8, 2022, 11:40 p.m.