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EGAN: Exploratory Gene Association Networks. Leverage organic intelligence.

EGAN: Exploratory Gene Association Networks. Is a software tool that allows a bench biologist. To visualize and interpret the results of high-throughput exploratory assays in an interactive hypergraph of genes. Protein-protein interactions, literature co-occurrence, etc. Annotation, signaling pathways, etc. EGAN provides comprehensive, automated calculation of meta-data coincidence. For user- and assay-defined gene lists. And provides direct links to web resources and literature. And follow along with th...

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EGAN: Exploratory Gene Association Networks. Leverage organic intelligence. | akt.ucsf.edu Reviews

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EGAN: Exploratory Gene Association Networks. Is a software tool that allows a bench biologist. To visualize and interpret the results of high-throughput exploratory assays in an interactive hypergraph of genes. Protein-protein interactions, literature co-occurrence, etc. Annotation, signaling pathways, etc. EGAN provides comprehensive, automated calculation of meta-data coincidence. For user- and assay-defined gene lists. And provides direct links to web resources and literature. And follow along with th...

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6 transcriptomics

7 genomics

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10 in silico analysis

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EGAN: Exploratory Gene Association Networks. Leverage organic intelligence. | akt.ucsf.edu Reviews

https://akt.ucsf.edu

EGAN: Exploratory Gene Association Networks. Is a software tool that allows a bench biologist. To visualize and interpret the results of high-throughput exploratory assays in an interactive hypergraph of genes. Protein-protein interactions, literature co-occurrence, etc. Annotation, signaling pathways, etc. EGAN provides comprehensive, automated calculation of meta-data coincidence. For user- and assay-defined gene lists. And provides direct links to web resources and literature. And follow along with th...

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EGAN: Exploratory Gene Association Networks. Leverage organic intelligence.

http://akt.ucsf.edu/EGAN/downloads.php

All versions of EGAN require the latest version of Java with Java WebStart. EGAN runs on most operating systems ( Windows, Mac, Linux. And is provided for use according to the terms of this license. For EGAN 1.5, you will need a minimum of 4GiB of free memory. 8GiB total memory) on your system in order to run human. EGAN, and it is recommended that you have at least 8GiB of free memory ( 16GiB total memory) for best performance. The demos are configured to require only 2GiB of free memory. Launch EGAN Sa...

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EGAN: Exploratory Gene Association Networks. Leverage organic intelligence.

http://akt.ucsf.edu/EGAN/screenshots.php

Click on each thumbnail for a full-size image). EGAN contains a point-and-click wizard to help the user load custom/proprietary data sets formatted using other software such as Microsoft Excel. EGAN allows dynamic gene list construction via combination of analysis results from multiple experiments and technology platforms; don't be constrained by ad-hoc p-value/FDR cutoffs! EGAN automatically generates comprehensive gene set enrichment statistics for your gene lists and experiment results. EGAN can assis...

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EGAN: Exploratory Gene Association Networks. Leverage organic intelligence.

http://akt.ucsf.edu/EGAN/leverage.php

Only a trained biologist can understand the semantic context of the experiment. As well as the semantic meaning of enriched meta-data. Annotation, signaling pathways, etc. And gene-gene relationships ( protein-protein interactions, literature co-occurrence, etc. And that biologist will have to make a significant commitment of time and/or funds to carry out follow-up experiments. EGAN has been designed to put the organic intelligence of the biologist in control of the exploratory analysis process by:.

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EGAN: Exploratory Gene Association Networks. Leverage organic intelligence.

http://akt.ucsf.edu/EGAN/documentation.php

Please visit UCSF EGAN Discussions. To post comments/questions and search archived discussions. EGAN Basic Ideas and Terminology. Version 1.4, PPT) - July 2010. EGAN Basic Ideas and Terminology. Version 1.4, PDF) - July 2010. EGAN tutorial: A basic use-case. Version 1.3, PPT) - July 2010. EGAN tutorial: A basic use-case. Version 1.3, PDF) - July 2010. EGAN tutorial: Interface basics. Version 1.1, PPT) - October 2009 by Jesse Paquette. EGAN tutorial: Loading network data. PPT) - July 2010. PDF) - July 2010.

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EGAN: Exploratory Gene Association Networks. Leverage organic intelligence.

http://akt.ucsf.edu/EGAN/why.php

EGAN functionality is comparable to a number of different software programs, from free-academic to enterprise-commercial. Here is a short list of what makes EGAN stand apart from the rest:. EGAN is free for use in academic research. EGAN is built for use by bench biologists. Not programmers (but even programmers will find it saves time and effort). Read more at Leverage Organic Intelligence. All EGAN functionality is presented via a consistent and streamlined user interface. EGAN can perform both GSEA.

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Pondering blather: Data mining talks

http://ponderingblather.blogspot.com/2010/07/data-mining-talks.html

The ramblings of a slightly disgruntled, but mostly not, bleeding heart liberal academic. Monday, July 19, 2010. Why has the quality of the now dozens of such talks I've suffered through been so low? Why should I care? I can't explain why this happens. Obviously it shouldn't. Perhaps it's a function of the relatively immature nature of bioinformatics as a field. It's still at a stage where method development. Application of the intelligent kind. I've heard through the grapevine that getting a grant to do...

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CBC: Software and Computing Resources

http://cbc.ucsf.edu/software/index.html

University of California San Francisco. UCSF Computational Biology Core (CBC). Software and Computing Resources. We contribute to several open-source projects including R. And core member Henrik Bengtsson is the creator of the Aroma Project. Being parts of these projects helps us to keep up to date with the field and to get invaluable feedback on our own software and work. Here are some of the software tools that we have developed ourselves or contributed to:. Preprocessing of spotted microarray data.

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akt.ucsf.edu

EGAN: Exploratory Gene Association Networks. Leverage organic intelligence.

EGAN: Exploratory Gene Association Networks. Is a software tool that allows a bench biologist. To visualize and interpret the results of high-throughput exploratory assays in an interactive hypergraph of genes. Protein-protein interactions, literature co-occurrence, etc. Annotation, signaling pathways, etc. EGAN provides comprehensive, automated calculation of meta-data coincidence. For user- and assay-defined gene lists. And provides direct links to web resources and literature. And follow along with th...

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