ExpHunterSuite

DOCUMENTATION - VIGNETTES

Link to ExpHunterSuite Vignettes

DOCUMENTATION - README

DEgenes Hunter

Protocol to undertake the key steps in the analysis of transcriptomics experiments, including differentially expressed gene detection, a co-expression analysis and the functional enrichment.

REQUIREMENTS

• R version 4

INSTALLATION

Install latest R-Version

Go to page https://cran.r-project.org and install the latest R version on your computer.

Install DEgenes Hunter from console (using devtools)

To install DEgenes Hunter from console, we use the devtools utility to install R packages from GitHub. Please type the following commands:

    Rscript -e 'install.packages("devtools", repos="http://cran.us.r-project.org")'
    Rscript -e 'devtools::install_github("seoanezonjic/ExpHunterSuite", dependencies=TRUE)'

Sometimes reactome.db download fails because this package is too large (>400 Mb) and R has a download timeout of 60 seconds by default.

    Rscript -e "getOption('timeout')"
        [1] 60

This error can be solved by installing reactome.db from source or extending the timeout threshold before installing the ExpHunterSuite package with the command:

    Rscript -e 'options(timeout=1000); devtools::install_github("seoanezonjic/ExpHunterSuite")'

Then, please create the folder where you want to install the command line scripts, copy the scripts there and make them command line accesible using these commands:

    mkdir install_folder
    Rscript -e "ExpHunterSuite::install_DEgenes_hunter('install_folder')"
    export PATH=path_to_install_folder:$PATH

This export PATH can also be added to the .bashrc or .bash_profile files.

REFERENCES AND CITATION

Please cite ExpHunterSuite as:

Jabato, F., Córdoba-Caballero, J., Rojano, E., Romá-Mateo, C., Sanz, P., Pérez, B., Gallego, D., Seoane, P., Ranea, J., and Perkins, J. 2021. Gene expression analysis method integration and co-expression module detection applied to rare glucide metabolism disorders using ExpHunterSuite. Scientific Reports 2021 11:1, 11(1), p.1–12. doi:http://dx.doi.org/0.1038/s41598-021-94343-w

Isabel González Gayte, Rocío Bautista Moreno, Pedro Seoane Zonjic and Manuel G. Claros (2017). DEgenes Hunter - A Flexible R Pipeline for Automated RNA-seq Studies in Organisms without Reference Genome. Genomics And Computational Biology , 3(3), e31. doi:http://dx.doi.org/10.18547/gcb.2017.vol3.iss3.e31