compared with
Current by Louis Felix Nothias
on May 07, 2018 14:57.

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Separate documentation is available for both [Molecular Networking Analysis|https://bix-lab.ucsd.edu/display/Public/Molecular+Networking+Analysis+Documentation] and [Cytoscape 2.8|https://bix-lab.ucsd.edu/display/Public/Cytoscape+2.8.X+Visualization+and+Analysis+Documentation] and [Cytoscape 3.2|https://bix-lab.ucsd.edu/display/Public/Cytoscape+3.2.X+Visualization+and+Analysis+Documentation]





h3. Citation





If you use MS-Cluster in your molecular networks, cite the following also: Frank, Ari M., et al. "Clustering millions of tandem mass spectra." Journal of proteome research 7.01 (2007): 113-122. [http://pubs.acs.org/doi/abs/10.1021/pr070361e|http://pubs.acs.org/doi/abs/10.1021/pr070361e]





h3. Data Analysis on GNPS



h5. Importing Public Datasets to Analyze

From the *Select Input Files* popup, you will be a shares files tab. There you will find a box called *Import Data Share*. In this box you may enter an accession of a MassIVE dataset. Upon clicking import the dataset will appear in your workspace to select input files to analyze from.

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h3. Selecting Data Input Files

h3. Metadata table in GNPS

The metadata file describes the samples properties and allows more flexibility for data analysis and visualization than selecting data input files within the workflow of GNPS (G1, G2, etc).

*Metadata table*. [More information here|https://bix-lab.ucsd.edu/display/Public/Metadata+table+in+GNPS#MetadatatableinGNPS-MetadatatableinGNPS] \[Recommended format\].
h5. Cytoscape

To learn how to create basic networks in Cytoscape see [here|https://bix-lab.ucsd.edu/display/Public/Cytoscape+3.4+Visualization+and+Analysis+Documentation] [here|https://bix-lab.ucsd.edu/display/Public/Cytoscape+3.6.1+Visualization+and+Analysis+Documentation]






h5. Analysis in GNPS