RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis

Developed by

in collaboration with

RNAdetector is a user-friendly software for the analysis of protein-coding genes and ncRNAs from RNA-Seq data. It can be run as stand-alone application or as a cloud based system.

Performed analyses

RNAdetector allows to perform several types of analysis such as:

Quantification and normalization
Differential expression analysis
miRNA-sensitive topological pathway analysis.

RNAdetector supports any organisms whose genomes\transcriptoms have been sequenced. However, some commonly studied species such as Human, Mouse, and C.elegans are available for download in our remote repository. The list of organisms will keeped updated.

Any other organisms can be easily added by uploading their genomes and\or transcriptomes and the genomic coordinates of the RNA molecules intended to be analyzed following the step-by-step procedures detailed in the user interface.

Non-coding RNAs analyzed

In addition to mRNAs, RNAdetector can also analyze several classes of small and long ncRNAs. Specifically, for Human, Mouse and C.elegans RNA-Seq data the following ncRNA classes can be analyzed:

Small non-coding RNAs

micro RNAs (miRNAs)
PIWI-associated RNAs (piRNAs)
Small nucleolar RNAs (snoRNAs)
tRNA derived small ncRNAs (tRFs and tsRNAs)
Long non-coding RNAs
long non-coding RNAs (lncRNAs)
transcribed UltraConserved Regions (tUCRs) (only for human)
circular RNAs (circRNAs)

The genomic annotations of all these above-mentioned classes of ncRNAs are already available for downloading from our remote repository. However, additional ncRNAs classes for human and other organism can be analyzed by uploading their genomic annotation or indexed transcriptome on RNAdetector following the step-by-step procedures detailed in the user interface. Therefore, any class of ncRNAs of any biological species can be analyzed by RNAdetector.

Features

RNAdetector has several features such as:

Easy installation and dependencies management
Cross-platform (Windows Professional, macOS, Ubuntu) and deployable as cloud-based system
Remotely controllable
Graphical User Interface (GUI)
Interactive graphical reports with the results of the analysis
RNAdetector installation

Detailed information concerning the system requirements and installation can be found in the wiki section

Installation on Windows Professional
Install Docker Desktop in your computer by downloading the installer at this link Docker Desktop
Once the installer has been downloaded, then double-click Docker Desktop Installer.exe to run it.
When prompted, select "Enable Hyper-V Windows Features" option in the Configuration page.
Follow the instructions on the installation wizard to authorize the installer and proceed with the installation.
When the installation has been done successfully, click Close to complete Docker installation process.
Now that Docker Desktop is installed, it is possible to proceed with RNAdetector installation by downloading its installer RNAdetector installer and following the instructions through the installation wizard.
RNAdetector is installed! Now, you will find RNAdetector in your application list.

Installation on macOS

Before proceed with Docker Desktop installation, check the system requirements at this link
Install Docker Desktop in your computer by downloading the installer at this link Docker Desktop
Once the installer has been downloaded, then run the Docker.dmg installer, and drag and drop the Docker icon the Applications folder.
Now that Docker Desktop is installed, it is possible to proceed with RNAdetector installation by downloading its installer RNAdetector installer and following the instructions through the installation wizard.
Drag and drop the RNAdetector icon to the Applications folder to complete the installation.
RNAdetector is installed! Now, you will find RNAdetector in your application list.

Installation on Ubuntu

Open terminal.

Install Docker in your computer by writing the following commands in your terminal (one by one).

curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add
sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu $(lsb_release -cs) stable"
sudo apt-get update
sudo apt-get install docker-ce docker-ce-cli containerd.io

Set your user name in Docker. If you do not know your user name, write the following command whoami in your terminal.
```
sudo usermod -aG docker YOUR_USER_NAME
```
Log out and log in from Ubuntu.
Download the RNAdetector.deb file from RNAdetector web site.
Open again the terminal and install RNAdetector by writing the following command.
```
sudo dpkg -i RNAdetector.deb
```
RNAdetector is installed! Now, you can find RNAdetector in your application list.

RNAdetector user guide

RNAdetector allows users to perform several RNA-Seq data analysis by using our intuitive GUI. Users can select from the dashboard:

Small RNA-Seq analysis for the analysis of small RNA-Seq data. It can be used for identification and quantification of small ncRNAs such as miRNAs, piRNAs, tRFs, and tsRNAs.
RNA-Seq analysis for the analysis of standard RNA-Seq data. It can be used for the identification and quatification of RNA species longer than 200 nt such as mRNAs, lncRNAs, and tUCR.
Circular RNA analysis for identification and quantification of circRNAs.

Once one of the abovementioned analysis is performed, it is possibile to execute downstream analysis such as:

Differential expression analysis to compare difference in the expression profile of such RNA molecules between case vs control samples;
Pathway analysis to execute a miRNA-sensitive topological pathway analysis on the results obtained by the differential expression analysis. However, currently only the differentially expressed mRNAs and miRNAs can be analyzed.

A more detailed user guide is available in the wiki section

Cite us

if you use RNAdetector cite: La Ferlita A, Alaimo S, Di Bella S, Martorana E, Laliotis GI, Bertoni F, Cascione L, Tsichlis PN, Ferro A, Bosotti R, Pulvirenti A. RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis. BMC Bioinformatics. 2021 Jun 3;22(1):298. doi: 10.1186/s12859-021-04211-7.

Contact us

Alessandro La Ferlita (alessandro.laferlita@unict.it)

Salvatore Alaimo (alaimos@dmi.unict.it)

Alfredo Pulvirenti (alfredo.pulvirenti@unict.it)

knowmics-lab / RNAdetector

readme