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JMP Genomics 5 released

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Close to the launch of JMP9 with it’s R integration comes the announcement of JMP Genomics 5 released. The product brief is available here http://jmp.com/software/genomics/pdf/103112_jmpg5_prodbrief.pdf and it has an interesting mix of features. If you want to try out the features you can see http://jmp.com/software/license.shtml

As per me, I snagged some “new”stuff in this release-

  • Perform enrichment analysis using functional information from Ingenuity Pathways Analysis.+
  • New bar chart track allows summarization of reads or intensities.
  • New color map track displays heat plots of information for individual subjects.
  • Use a variety of continuous measures for summarization.
  • Using a common identifier, compare list membership for up tofive groups and display overlaps with Venn diagrams.
  • Filter or shade segments by mean intensity, with an optionto display segment mean intensity and set a reference valuefor shading.
  • Adjust intensities or counts for experimental samples using paired or grouped control samples.
  • Screen paired DNA and RNA intensities for allele-specific expression.
  • Standardize using a shifting factor and perform log2transformation after standardization.
  • Use kernel density information in loess and quantile normalization.
  • Depict partition tree information graphically for standard models with new Tree Viewer
  • Predictive modeling for survival analysis with Harrell’s assessment method and integration with Cross-Validation Model Comparison.

That’s right- that is incorporating the work of our favorite professor from R Project himself- http://biostat.mc.vanderbilt.edu/wiki/Main/FrankHarrell

Apparently Prof Frank E was quite a SAS coder himself (see http://biostat.mc.vanderbilt.edu/wiki/Main/SasMacros)

Back to JMP Genomics 5-

The JMP software platform provides:

• New integration capabilities let R users leverage JMP’s interactivegraphics to display analytic results.

• Tools for R programmers to build and package user interfaces that let them share customized R analytics with a broader audience.•

A new add-in infrastructure that simplifies the integration of external analytics into JMP.

 

+ For people in life sciences who like new stats software you can also download a trial version of IPA here at http://www.ingenuity.com/products/IPA/Free-Trial-Software.html


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