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
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.
- 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
-
For window users :
User need to install Rtools before installing tReasure. -
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
-
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+
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()
- 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()
library("tReasure")
tReasure::tReasure()
- 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
- Small RNA-seq dataset from human breast tissues (part of GSE68085)
- Download
- Control (Normal): SRR1982473, SRR1982474, SRR1982475
- Test (Cancer): SRR1982580, SRR1982581, SRR1982582