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BioGoggles is a freely available, open source Bioinformatics software package developed by Bio-Compute, Inc. for visualization and analysis of high-throughput molecular profiling experiments. BioGoggles has two main components, a GUI tool for displaying the data and its analysis, and a Java based CLI tool for automated data retrieval and analysis. BioGoggles is open source and open development at GitHub. BioGoggles runs on Windows, Mac OS, and Linux operating systems and is open source software under the MIT License. BioGoggles is free software released under the GNU Affero General Public License version 3.
BioGoggles is an add-on to the open source Bio-Compute cloud based computational platform, which has been successfully used to analyze data from several high-throughput microarray experiments. By providing a graphical interface for analyzing microarray data, BioGoggles enables non-programmers to explore high-dimensional data sets without programming experience. BioGoggles can be used for standard data analysis tasks including but not limited to finding marker genes, differentially expressed genes, rank order genes, clustering of genes.  BioGoggles also enables the discovery of differentially expressed pathway genes, the use of meta-genomics information such as co-expression of genes.
Biogoggles is written in Java and can be used on Windows, Mac OS, and Linux operating systems. BioGoggles is open source software under the GNU Affero General Public License version 3, and development is available on GitHub.
See also
Biomedical informatics
Genetics
Omics
Omics data
Omics data management
Biomedical Informatics
Bioinformatics
References
External links
 BioGoggles homepage
 Bio-Compute homepage
Category:Bioinformatics software
Category:Science software for Windows
Category:Science software for MacOS
Category:Science software for Linux
Category:Science software for Linux
Category:Free bioinformatics softwareQ:
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BioGoggles analysis performs a 5-step process for data normalization, filtering, correlation discovery, and variable ranking:
1. Normalization
Standardizes data to allow comparisons between samples
2. Correlation Discovery
Sets up a correlation threshold for detecting correlations among variables
3. Filtering
Sets up a filter for finding the top few variables or items
4. Correlation Feature Ranking
Assigns a rank to each filtered item based on correlation strength and spread
5. Gene/Biomarker Discovery
Discovers genes or biomarkers based on the correlation features
BioGoggles Output:
BioGoggles generates the following visualization output:
Visualization by applying thresholds and creating layers:
BioGoggles Analysis Detail:
When running BioGoggles analysis, an Excel spreadsheet is generated with the following columns:
Column 1
Column 2
Column 3
Column 4
Column 5
Column 6
Column 7
Column 8
Column 1 and Column 2 will be the input files (CVS or txt format).
Column 3, Column 4, Column 5 and Column 6 are the names of the two variables being explored in the data set.
Column 7 and Column 8 are the names of the two groups.
This Excel spreadsheet will show either a scatter plot or heat map of the data.
The Excel will be saved in a folder called "Analysis"
How to run BioGoggles Analysis?
See BioGoggles website for installation instructions. There are 3 different modes:
Personal – for development and debugging
Web application – web application for the automatic analysis of data sets available.
Server – web application for the automatic analysis of data sets on a public server
After installation, if you want to run BioGoggles on your data set you can follow one of the following:
BioGoggles Manual
BioGoggles Web Application
BioGoggles Web Server
BioGoggles Manual requires installation of BioGoggles software.
Once installed, BioGoggles Manual can be run from command line or from a windows application.BioGoggles Web Application can be automatically launched from the web browser in case of running your data set on a public server.
BioGoggles Web Server can be used to run BioGoggles analysis on a data set on your computer. You don't need BioGoggles application to access the server.
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