<html><head><meta name="color-scheme" content="light dark"></head><body><pre style="word-wrap: break-word; white-space: pre-wrap;"># geoCancerDiagnosticDatasetsRetriever
GEO Cancer Diagnostic Datasets Retriever is a bioinformatics tool for cancer diagnostic dataset retrieval from the GEO website.
## Summary
&lt;p&gt;Gene Expression Omnibus (GEO) Cancer Diagnostic Datasets Retriever is a Bioinformatics tool for cancer diagnostic dataset retrieval from the GEO database. It requires a GeoDatasets input file listing all GSE dataset entries for a specific cancer (for example, Myelodysplastic syndrome), obtained as a download from the GEO database. This Bioinformatics tool functions by applying keyword filters to examine individual GSE dataset entries listed in a GEO DataSets input file. The first Diagnostic text filter flags for diagnostic keywords (for example, 窶彭iagnosis窶� or 窶徂ealth窶�) used by clinical science researchers and present in the title/abstract entries. Next, a flagged dataset is examined (by a second Diagnostic text filter) for diagnostic keywords, which may be present in the "Overall design" section of a GSE dataset. If found, this tool outputs the GSE code of the likely diagnostic dataset. If not found by the second filter, a more intensive filtering stage is performed. Here, this tool runs an R script (healthyControlsPresentInputParams.r) whose function is to detect desired keywords in the .SOFT file of this dataset and identify if it is a likely diagnostic dataset.&lt;/p&gt;

## Installation
geoCancerDiagnosticDatasetsRetriever can be used on any Linux or macOS machines. To run the program, you need to have the following programs installed on your computer:

&lt;p&gt;&lt;ul&gt;&lt;li&gt;&lt;b&gt;Perl&lt;/b&gt; (version 5.8.0 or later)&lt;/li&gt;&lt;/ul&gt;&lt;/p&gt;
&lt;p&gt;&lt;ul&gt;&lt;li&gt;&lt;b&gt;cURL&lt;/b&gt; (version 7.68.0 or later)&lt;/li&gt;&lt;/ul&gt;&lt;/p&gt;
&lt;p&gt;&lt;ul&gt;&lt;li&gt;&lt;b&gt;Lynx&lt;/b&gt; (version 2.9.0dev.5 or later)&lt;/li&gt;&lt;/ul&gt;&lt;/p&gt;
&lt;p&gt;&lt;ul&gt;&lt;li&gt;&lt;b&gt;R programming language&lt;/b&gt; (version 4 or later)&lt;/li&gt;&lt;/ul&gt;&lt;/p&gt;
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 or Lynx on macOS. They would need to be manually installed through your operating system's software centres. cURL and Lynx will be installed automatically on Linux Ubuntu by geoCancerDiagnosticDatasetsRetriever.
&lt;p&gt;&lt;/p&gt;

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 to manually install the libfile-homedir-perl
package (`sudo apt-get install -y libfile-homedir-perl`), if not
already installed in your Perl 5 configuration.

CPAN install:

```diff
cpanm App::geoCancerDiagnosticDatasetsRetriever
```

To uninstall:

```diff
cpanm --uninstall App::geoCancerDiagnosticDatasetsRetriever
```
On Linux Ubuntu, you might need to run the two previous CPAN commands as a superuser (`sudo cpanm App::geoCancerDiagnosticDatasetsRetriever` and `sudo cpanm --uninstall App::geoCancerDiagnosticDatasetsRetriever`).

## Data file
The required input file is a GEO DataSets file obtainable as a download  from &lt;a href="https://www.ncbi.nlm.nih.gov/gds/" target="_blank" rel="noopener noreferrer"&gt;GEO DataSets&lt;/a&gt;, upon querying for any particular cancer (for example, myelodysplastic syndrome) in geoCancerDiagnosticDatasetsRetriever.

## Execution instructions
Run geoCancerDiagnosticDatasetsRetriever with the following command:

```diff
geoCancerDiagnosticDatasetsRetriever -d "CANCER_TYPE" -p "PLATFORMS_CODES"
```

An example command using "myelodysplastic syndrome" as a query: 

```diff
geoCancerDiagnosticDatasetsRetriever -d "myelodysplastic syndrome" -p "GPL570"
```

The input and output files of geoCancerDiagnosticDatasetsRetriever will be found in the `~/geoCancerDiagnosticDatasetsRetriever_files/data/` and `~/geoCancerDiagnosticDatasetsRetriever_files/results/` directories, respectively.

&lt;p&gt;Help information can be read by typing the following command:&lt;/p&gt;  

```diff
geoCancerDiagnosticDatasetsRetriever -h
```

&lt;p&gt;This command will print the following instructions:&lt;/p&gt;

```diff
Usage: geoCancerDiagnosticDatasetsRetriever -h

Mandatory arguments:
  CANCER_TYPE           type of the cancer as query search term
  PLATFORM_CODES        list of GPL platform codes

  Optional arguments:
  -h                    show help message and exit
  ```

## Copyright and License

Copyright 2021 by Abbas Alameer (Kuwait University) and Davide Chicco (University of Toronto)

This program is free software; you can redistribute it and/or modify
it under the terms of the &lt;a href="http://www.gnu.org/licenses/gpl-2.0-standalone.html" target="_blank" rel="noopener noreferrer"&gt;GNU General Public License, version 2 (GPLv2).&lt;/a&gt;

## Contact
&lt;p&gt;geoCancerDiagnosticDatasetsRetriever was developed by:&lt;br&gt;
&lt;a href="http://kuweb.ku.edu.kw/biosc/People/AcademicStaff/Dr.AbbasAlameer/index.htm" target="_blank" rel="noopener noreferrer"&gt;Abbas Alameer&lt;/a&gt; (Kuwait University) and &lt;a href="http://www.DavideChicco.it" target="_blank" rel="noopener noreferrer"&gt;Davide Chicco&lt;/a&gt; (University of Toronto)&lt;/br&gt;

For information, please contact Abbas Alameer at abbas.alameer(AT)ku.edu.kw or Davide Chicco at davidechicco(AT)davidechicco.it&lt;/p&gt;
</pre></body></html>