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UNLABELLED: Gene Set Enrichment Analysis (GSEA) is a computational method that assesses whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states. We report the availability of a new version of the Java based software (GSEA-P 2.0) that represents a major improvement on the previous release through the addition of a leading edge analysis component, seamless integration with the Molecular Signature Database (MSigDB) and an embedded browser that allows users to search for gene sets and map them to a variety of microarray platform formats. This functionality makes it possible for users to directly import gene sets from MSigDB for analysis with GSEA. We have also improved the visualizations in GSEA-P 2.0 and added links to a new form of concise gene set annotations called Gene Set Cards. These additions, as well as other improvements suggested by over 3500 users who have downloaded the software over the past year have been incorporated into this new release of the GSEA-P Java desktop program.
AVAILABILITY: GSEA-P 2.0 is freely available for academic and commercial users and can be downloaded from http://www.broad.mit.edu/GSEA
Qlucore Omics Explorer is a D.I.Y next-generation bioinformatics software for research in life science, plant- and biotech industries, as well as academia. The powerful visualization-based data analysis tool with inbuilt powerful statistics delivers immediate results and provides instant exploration and visualization of big data.
Second, when I opened the downloaded.jnlp file, GSEA does open fine, but when the Load Data button is clicked on, there is no pop up window for input files. I have the latest Java (9.0) installed on my Mac (OS X 10.10). Any discussion on this will be appreciated! 2GB of free/system memory is needed to run GSEA or navigate through an Enrichment Map. Thus having at least 4GB of system memory is recommended. (you can check it in System Properties on a Windows machine and under About this Mac for mac computers) 2.5 GB is required to build and view an EnrichmentMap with Cytoscape 3.
SIMPLIFY YOUR GSEA ANALYSIS
The integrated Gene Set Enrichment Analysis (GSEA) workbench allows straightforward analysis of the biological context (pathways, ontology categories or any other relevant set of genes) in Qlucore Omics Explorer.
Compare your genes of interest Compare your genes of interest with pathways (typically gene sets) and quickly identify enriched pathways.
Gsea Software Download
Visualize the resulting pathways in Running Enrichment score plots, heatmaps and gene lists and leading-edge overlap plots. All the plots can be exported with one click.
The GSEA workbench is integrated and works side by side with the other functionality in the program making it easy and fast to test different approaches. The integration makes it possible to export gene lists (pathways) from the GSEA workbench to the variable list panel in the main program and continue detailed analysis of the underlying data based on the outcome of the GSEA analysis.
Gsea Gene Set Database
You can read more about Pathway analysis here.