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:

• strict

• warnings

• Term::ANSIColor

• Getopt::Long

• File::Basename

• File::HomeDir

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:

• Perl (version 5.8.0 or later)

• cURL (version 7.68.0 or later)

• R programming language (version 4 or later)

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:

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

sudo apt-get install -y libfile-homedir-perl

cpanminus

sudo apt -y install cpanminus

CPAN install:

cpanm App::easyDifferentialGeneCoexpressionWrapper

To uninstall:

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:

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:

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 <PROBESETS_OR_GENE_SYMBOLS>

A flag to indicate type of data (probesets or gene symbols) being read during execution

-f <INPUT_FILE>

The name of the CSV file listing the probesets or the gene symbols

-d <GEO_DATASET_CODE>

GEO dataset code of the microarray platform for which the probeset-gene symbol mapping should be done

-v <FEATURE_NAME>

Name of the feature of the dataset that contains the two conditions to investigate

-v1 <CONDITION_1>

Name of the first condition in the feature to discriminate (for example, "healthy")

-v2 <CONDITION_2>

Name of the second condition in the feature to discriminate (for example, "can- cer")

-o <OUTPUT_FILE>

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:

easyDifferentialGeneCoexpressionWrapper -h

This command will print the following instructions:

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