# easyDifferentialGeneCoexpressionWrapper easyDifferentialGeneCoexpressionWrapper is a wrapper program for the easyDifferentialGeneCoexpression.r R script (developed by Davide Chicco). ## Summary

This is a wrapper program for the easyDifferentialGeneCoexpression.r whose function is to detect pairings of genes/probesets with the highest, significant differential coexpression. For more information, (see this description manual).

## easyDifferentialGeneCoexpressionWrapper dependencies The dependencies (i.e. packages) used by easyDifferentialGeneCoexpressionWrapper are:

## Installation easyDifferentialGeneCoexpressionWrapper can be used on any Linux, macOS, or Windows machines. On the Windows operating system you will need to install the Windows Subsystem for Linux (WSL) compatibility layer (quick installation instructions). Once WSL is launched, the user can follow the easyDifferentialGeneCoexpressionWrapper installation instructions described below. To run the program, you need to have the following programs installed on your computer:

By default, Perl is installed on all Linux or macOS operating systems. Likewise, cURL is installed on all macOS versions. cURL/R may not be installed on Linux/macOS. They would need to be manually installed through your operating system's software centres. cURL will be installed automatically on Linux Ubuntu by easyDifferentialGeneCoexpressionWrapper.

Manual install: ```diff perl Makefile.PL make make install ``` On Linux Ubuntu, you might need to run the last command as a superuser (`sudo make install`) and you will need to manually install (if not already installed in your Perl 5 configuration) the following packages: libfile-homedir-perl ```diff sudo apt-get install -y libfile-homedir-perl ``` cpanminus ```diff sudo apt -y install cpanminus ``` CPAN install: ```diff cpanm App::easyDifferentialGeneCoexpressionWrapper ``` To uninstall: ```diff cpanm --uninstall App::easyDifferentialGeneCoexpressionWrapper ``` On Linux Ubuntu, you might need to run the two previous CPAN commands as a superuser (`sudo cpanm App::easyDifferentialGeneCoexpressionWrapper` and `sudo cpanm --uninstall App::easyDifferentialGeneCoexpressionWrapper`). ## Execution instructions The command for running easyDifferentialGeneCoexpressionWrapper is: ```diff easyDifferentialGeneCoexpressionWrapper -a "PROBESETS_OR_GENE_SYMBOLS" -f "INPUT_FILE" -d "GEO_DATASET_CODE" -v "FEATURE_NAME" -v1 "CONDITION_1" -v2 "CONDITION_2" -o "OUTPUT_FILE" ``` An example usage command for computing the differential coexpression of probesets in the (GSE30201 gene expression dataset) is: ```diff easyDifferentialGeneCoexpressionWrapper -a "PROBESETS" -f "dc_probeset_list03.csv" -d "GSE30201" -v "source_name_ch1" -v1 "Patient" -v2 "Normal" -o result.out ``` When using this command, the output files of easyDifferentialGeneCoexpressionWrapper will be found in the `~/easyDifferentialGeneCoexpressionWrapper_files/results/` directory, created in the user's home directory. The mandatory command line options are described below: -a A flag to indicate type of data (probesets or gene symbols) being read during execution -f The name of the CSV file listing the probesets or the gene symbols -d GEO dataset code of the microarray platform for which the probeset-gene symbol mapping should be done -v Name of the feature of the dataset that contains the two conditions to investigate -v1 Name of the first condition in the feature to discriminate (for example, "healthy") -v2 Name of the second condition in the feature to discriminate (for example, "can- cer") -o Name of the output file where the output data for the differential coexpression of probesets are written

Help information can be read by typing the following command:

```diff easyDifferentialGeneCoexpressionWrapper -h ```

This command will print the following instructions:

```diff Usage: easyDifferentialGeneCoexpressionWrapper -h Mandatory arguments: -a GENE_SYMBOLS -f user-specified CSV file -d GEO dataset code -v feature name -v1 condition 1 -v2 condition 2 -o output results file -h show help message and exit ``` ## Copyright and License Copyright 2022 by Abbas Alameer (Kuwait University) This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License, version 2 (GPLv2). ## Contact

easyDifferentialGeneCoexpressionWrapper was developed by:
Abbas Alameer (Kuwait University)
For information, please contact Abbas Alameer at abbas.alameer(AT)ku.edu.kw