JMP® Genomics 5: more ways to visualize, explore data
New version adds tabbed reports, customizable analysis options and integration with other tools
CARY, NC (Nov. 02, 2010) – JMP® Genomics now provides more freedom to explore, understand and share analysis results of genomics data sets. Version 5 of JMP Genomics, just released by business analytics leader SAS, features new ways to examine large data sets visually and interactively to detect hidden patterns.
JMP Genomics 5 introduces enhancements to almost all analysis areas. An elegant user interface organizes analysis results into tabbed reports and lets users customize the display of analysis options. Built on the new JMP 9 platform, JMP Genomics 5 also supports easy integration with the R open-source statistical programming language, Microsoft Excel and other tools.
"JMP Genomics makes it easy to conduct sophisticated genomic analyses. It's always a step ahead in adding new statistical techniques for analyzing novel data types," said Julien Ayroles, PhD, of the Department of Genetics at North Carolina State University. "Version 5 will make a bioinformatician out of even the most reluctant biologist."
"If I had to summarize JMP Genomics in one word, it would be 'simplicity.' I love the simple user interface and the fact that it offers one-stop shopping for any genomics analyses you're likely to need," said Joshua Banta, PhD, of New York University's Center for Genomics and Systems Biology. "If I were given another five words to summarize JMP Genomics, they would be 'you're not on your own.' The customer support from technical and statistical experts at JMP is simply unmatched in the software industry. If you don't know how to do an analysis, a live expert will walk you through it."
Here are highlights of new features:
Tabbed reports organize graphical output from analyses. Underlying data tables are hidden by default, with flexible options to open data or graphics in a new window to allow side-by-side comparisons.
Customizable JMP Genomics Starter mirrors the JMP Genomics menu and lets users customize profiles to view the processes they use frequently. Customized profiles can be exported or imported so groups can standardize on commonly used toolsets.
New JMP Genomics Wizard walks users through the import and analysis of new data sets. Users select a data type and the wizard provides step-by-step instructions for creating a design file and importing data and annotation information.
Interface with R lets R users display analytic results as interactive JMP graphics and access JMP and SAS Analytics. R programmers can also build user interfaces to deliver their programs to a broader audience.
Architecture for custom add-ins enables users to create JMP add-ins to enhance the capabilities of JMP and share within their organizations or at www.jmp.com/addins.
Updates to support next-gen data include import support for SAM files and new track types, such as histograms and heat plots. JMP Genomics 5 adds tools for analyzing and viewing summaries of next-gen data from various technologies. Support for rare variant summarization and analysis and new capabilities for allele-specific expression analysis will benefit users of both array technologies and those with summary data from next-gen studies.
New options for genetic analysis feature a new Q-K Workflow that streamlines association analysis while simultaneously correcting for population structure and sample relatedness. New processes help screen for interactions between pairs of SNPs or test associations between SNPs and multiple traits simultaneously. An experimental process allows estimation of linkage disequilibrium blocks for calculating haplotype frequencies within blocks.
Enrichment analysis provides new ways to integrate pathway information with statistical results. The new Get IPA Pathways function benefits users of JMP Genomics and Ingenuity Pathways Analysis, JMP's partner tool. JMP Genomics 5 also adds new tools to summarize individual expression deviations to identify significantly affected pathways.
JMP is a business unit of SAS, established in 1989 to create interactive software for desktop discovery analytics. John Sall, SAS co-founder and Executive Vice President, also heads the JMP business unit.
SAS is the leader in business analytics software and services, and the largest independent vendor in the business intelligence market. Through innovative solutions delivered within an integrated framework, SAS helps customers at more than 45,000 sites improve performance and deliver value by making better decisions faster. Since 1976 SAS has been giving customers around the world
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Multiway Venn diagrams in JMP Genomics let you visualize shared patterns, overlay statistical findings and drill down on the most important gene sets.