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
Read rest of the new software here http://jmp.com/software/genomics/pdf/103112_jmpg5_prodbrief.pdf
- JMP 9 releasing on Oct 12 (r-bloggers.com)
- New JMP Software Version Extends Analytic Options (eon.businesswire.com)
- Dan Ariely Headlines JMP Analytics Conference (eon.businesswire.com)
- Whole Genome Sequencing of Japanese Individual Reveals Wealth of Undiscovered Genetic Variation (prweb.com)
- Blog – Ozzy Osbourne’s Genome (technologyreview.com)
- SAS Continues to Expand Analytics Options with Additional R Integration (eon.businesswire.com)
- Human Genome Sciences Invites Investors to Listen to Webcast of Presentation at JMP Securities Healthcare Conference (eon.businesswire.com)
- SAS, JMP Mix Simulation and Analytics to Foster Innovation (eon.businesswire.com)
- Using JMP 9 and R together (r-bloggers.com)
- Japanese flower has the biggest genome in the world [Mad Genomics] (io9.com)
- JMP Customer Herzenberg Lab Wins Computerworld Honor (eon.businesswire.com)