mixOmics for 2016

Posted on March 16, 2016 by klecao

Well well, 2016 is well under way and we thought we could give you some heads up as of what is happening next for mixOmics.

2015 has been great for us:

  • We ran a total of 5 x 12-day mixOmics workshops (see list below, in Auckland NZ, Birsbane AUS, Paris, Montpellier and Toulouse, FR),
  • We launched our first shiny web-interface for sPLS-DA, which has been developed for our published paper (PCT patent ‘Blood Test for Throat Cancer’ PCT/AU2015/050723 on the biological findings of those interesting biomarkers). The shiny web-interface is still at its infancy, as we can only have one user at a time (shiny requirements!), and so if the interface goes grey, it means that someone else is using it!
  • Francois Bartolo, one mixOmics key developer from Toulouse, came to Brisbane for a 3-month visit and gave a good stab to most of the graphical functions (plotIndiv, network, CIM…)
  • Benoit Gautier, our key mixOmics developer based in Brisbane developed the shiny web-interface and set up the new sGCCA functions (integration of multiple data sets)
  • Benoit and Florian Rohart (also key mixOmics developer based in Brisbane) also worked together to push mixOmics V6.
  • We also made a good stab at our multivariate analysis pipeline for 16S microbial data, with a first unpublished workflow available here and a preprint available soon.

What’s planned for 2016?

  • More workshops! So far 3 are planned (those will be announced on our website)
  • We will clone few shiny web-interfaces on our virtual machine to enhance this tool.
  • mixOmics V6 is in the backlogs, with a planned update for end of April 2016 (stay tuned!) and we will (finally) push a proper mixOmics software manuscript.
  • We are in the process of reorganising a few workflows in mixOmics with:
    • mixMC: mixOmics for Microbial Communities (16S data)
    • mixDIABLO: a framework for Data Integration Analysis for Biomarker discovery using Latent variable approaches for multi-Omics studies (check out that acronym!)
    • mixMINT: mixOmics for Multi-group INTegrative studies to combine independent single ‘omics studies.

In short, there will be more functionalities for mixOmics users but it should not change the calls of the main functions and we are wrapping up the statistical developments that kept us busy in the last couple of years.

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List of 2015 workshops:

  • Oct 24-25 2015 (2 days) AgroParisTech, Paris, France. #attendees: 22
  • Sept 15-16 2015 (2 days) National Institute for Agricultural Research, Toulouse, France. #attendees: 16
  • Sept 10-11 2015 (2 days) CIRAD, Agriculture research for development, Montpellier, France. #attendees: 25 (full)
  • 13-14 August 2015 (2 days) Translational Research Institute, Brisbane Australia. #attendees: 32 (full)
  • April 9-10 2015 (2 days) University of Auckland, New Zealand. #attendees: 40 (full)
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