You can create and edit GSAASeqSP files using Excel or any text editor. You use the files on the Broad ftp site, export gene sets from the Molecular Signature Database (MSigDb) or create your own gene sets file. For each gene set, gives the gene set name and list of features (genes or probes) in that gene set. Only categorical labels are allowed in GSAASeqSP.Ĭontains one or more gene sets. Expression data can come from any source.Ĭontains phenotype labels and associates each sample with a phenotype. The count values must be raw counts of sequencing reads. All files are tab-delimited ASCII text files they can be created and edited using any text editor.Ĭontains gene names, samples, and a count for each gene in each sample. The following table lists each type of data file and its valid file formats. When you use GSAASeqSP, you supply three data files: an expression dataset file, a phenotype labels file, a gene sets file. If you cannot find the answers to your questions on our web site, contact us at Data Files for GSAASeqSP The web site provides a link to the paper describing the algorithms. The GSAASeqSP documentation includes this User Guide.Ģ. The GSAA web site is your primary source of help for GSAASeqSP. Click the close (x) button on the top-right corner of the GSAASeqSP window. To close the page, click the close (X) icon on the tab.ġ. To open GSAASeqSP page, click the icon "Run GSAASeqSP", GSAASeqSP tab will appear next to the Home tab. When you start GSAA, the main panel displays the Home page. The main panel on the right, which is used to display dialogs and results. The Processes panel in the bottom left corner, which provides information about the status of your analyses.ģ. The navigation bar on the left, which provides quick access to common GSAA operations.Ģ. The main components of the user interface are as follows:ġ. When GSAA starts, the main window appears. GSAASeqSP has been successfully used with 20000m on a Linux server.įull_path is the complete path of the GSAA.jar fileĮxample: Java –Xmx1000m –jar C:/programs/gsaa/GSAA.jar
If you get error message “out of memory”, try to increase 1000m to 2000m or more. Parameter –Xmx specifies the amount of memory available to Java. To launch GSAA, double click the icon of GSAA.jar file or use command Remember, lib and GSAA.jar must be in the same directory. Unzip or untar the downloaded program file into a directory.
GSAASeqSP can run on any computer (Windows, Mac OS X, Linux etc.) that supports Java7+.
Software GSAASeqSP is released as a functionally independent module in our GSAA platform that is available for free download at GSAASeqSP: A toolset for gene set association analysis of RNA-Seq data. The software GSAASeqSP is a Java based desktop application which implements methods described in GSAASeqSP identify pathways/gene sets significantly associated with a disease or a phenotype by analyzing genome-wide patterns of gene expression variation measured by RNA-Seq technology.
Gene Set Association Analysis for RNA-Seq with Sample Permutation (GSAASeqSP) is a toolset for gene set association analysis of RNA-Seq count data.