TuxNet

MATLAB app to process raw RNA sequencing data and infer gene regulatory networks. Published and maintained by Sozzani Lab at North Carolina State University.

Table of Contents

• Local Installation
  • MATLAB Version
  • Mac Standalone Version
  • Linux Standalone Version
  • Windows Standalone Version
  • Required Software
  • Video Tutorial
• TUX
• GENIST
• RTP-STAR
• Additional Info

Local Installation

MATLAB Version

The use of the MATLAB version of TuxNet requires a 64-bit computer running Mac or Linux with MATLAB installed (R2017b up until R2022a). In addition, two MATLAB toolboxes need to be installed: the Bioinformatics toolbox and the Statistics and Machine Learning toolbox.

Download the files from the project repository and unzip. To run TuxNet using Arabidopsis data, unzip genome.fa.zip.

To use the MATLAB version of TuxNet, run TuxNet.mlapp ub the TuxNet-MATLAB directory.

Mac Standalone Version

The use of the Mac Standalone version of TuxNet requires a 64-bit computer but does not require a MATLAB installation.

Download the files from the project repository and unzip. To run TuxNet using Arabidopsis data, unzip genome.fa.zip.

To install, run TuxNet-MacStandaloneInstaller.app in the TuxNet-MacStandalone directory. You will be prompted to choose a directory where TuxNet will be installed and to install MATLAB Runtime if it is not already installed.

To use TuxNet, run TuxNet.app in the <TuxNetLocation>/application directory where <TuxNetLocation> is the directory where you chose to install TuxNet. You will be prompted to choose the current working directory via a file finder: <TuxNetLocation>/application should be your selection.

Linux Standalone Version

The use of the Linux Standalone version of TuxNet requires a 64-bit computer but does not require a MATLAB installation.

Download the files from the project repository and unzip. To run TuxNet using Arabidopsis data, unzip genome.fa.zip.

To install, execute sudo ./TuxNet-LinuxStandaloneInstaller.install in the TuxNet-LinuxStandalone directory. You will be prompted to choose a directory where TuxNet will be installed and to install MATLAB Runtime if it is not already installed.

To use TuxNet, navigate to the <TuxNetLocation>/application directory where <TuxNetLocation> is the directory where you chose to install TuxNet and execute sudo ./run_TuxNet.sh <mcr_directory> where <mcr_directory> is the location where MATLAB Runtime is installed. For example: sudo ./run_TuxNet.sh /home/user/username/MATLAB_Runtime/v96. You will be prompted to choose the current working directory via a file finder: <TuxNetLocation>/application should be your selection.

Windows Standalone Version

Download the files from the project repository and unzip. NOTE: TuxNet Windows Standalone Version is only tested with Windows 10 and higher.

To install, run TuxNet-WindowsStandaloneInstaller.exe in the TuxNet-WindowsStandalone directory. You will be prompted to choose a directory where TuxNet will be installed and to install MATLAB Runtime if it is not already installed. Note that the Windows Standalone version of TuxNet cannot run the modified Tuxedo pipeline.

To use TuxNet, run TuxNet.exe in the <TuxNetLocation>/application directory where <TuxNetLocation> is the directory where you chose to install TuxNet. You will be prompted to choose the current working directory via a file finder: <TuxNetLocation>/application should be your selection.

Required Software

HISAT2, Cufflinks, ea-utils, and SAMtools must be installed before the TUX tab can be run using TuxNet on the MATLAB, Mac Standalone, and Linux Standalone versions. Once these are downloaded and installed, you must copy the folders into the directory where TuxNet is located and change the folder names to hisat2, cufflinks, ea-utils, and samtools, respectively. Otherwise, TuxNet will not be able to find the needed files.

Video Tutorial

Follow this tutorial to learn how to install and run the MATLAB and Standalone versions of TuxNet for Mac. The steps to install the Linux and Windows versions are similar and require only slight modification, detailed above.

TUX

The TUX tab processes raw RNAseq data using fastq-mcf and a modified Tuxedo pipeline (HISAT2 + Cufflinks package) to extract a wide array of information including measures of differential expression. This output can then be used by TuxOP to tabulate FPKM values, average gene expression, and differentially expressed genes (DEGs) between states of an experiment.

GENIST

The GENIST tab implements a Dynamic Bayesian network (DBN)-based inference algorithm that uses time-course data to infer GRNs for a list of genes. The output of TUX can be directly imported into GENIST to predict causal relations and the output of GENIST can be imported into programs like Cytoscape for visualization.

RTP-STAR

The RTP-STAR tab implements a regression tree algorithm (GENIE3) and uses biological replicates of steady state gene expression data to infer GRNs for a list of genes. The output of TUX can be directly imported into RTP-STAR to predict causal relations and the output of RTP-STAR can be imported into programs like Cytoscape for visualization.

Additional Info

More details on running the software are provided in the following manuscript: TuxNet: A simple interface to process RNA sequencing data and infer gene regulatory networks

Please contact Dr. Lisa Van den Broeck at lfvanden@ncsu.edu or Dr. Ross Sozzani at ross_sozzani@ncsu.edu with any questions or issues.

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HOW TO CITE: Spurney, R.J., Van den Broeck, L., Clark, N.M., Fisher, A.P., de Luis Balaguer, M.A. and Sozzani, R. (2019), Tuxnet: a simple interface to process RNA sequencing data and infer gene regulatory networks. Plant J. https://doi.org/10.1111/tpj.14558