Category: Workshop

Software requirements for mixOmics workshops

We list below some installation requirements to ensure the mixOmics workshop will run smoothly for everyone.

Important reminders. We expect the trainees to have a good working knowledge in R programming (e.g. handling data frame, perform simple calculations and display simple graphical outputs) to be able to fully enjoy the workshop. Attendees are requested to bring their own laptop as this is a hands-on workshop (we will alternate theory and practice).

Software installation and updates. To run the R scripts in this workshop, you will need to install or update the latest versions of R available from the CRAN (currently > 3.4, see also Installation guide for R and RStudio), followed by the update or installation of the following R packages:

  • mixOmics version 6.3.1 (the version number is important)
  • mvtnorm
  • corrplot
  • igraph

The mixOmics package should directly import the following packages: igraph, rgl, ellipse, corpcor, RColorBrewer, plyr, parallel, dplyr, tidyr, reshape2, methods , matrixStats , rARPACK, gridExtra .

Check after install that the following does not throw any error*:

library(mixOmics)

We also advise to use the software RStudio

*For apple mac users, if you are unable to install the mixOmics imported library rgl, you will need to install the XQuartz software first .

Wifi will be available on site, but it is preferable that you make those installations before the workshop to avoid delays for the analyses.

Any question regarding the requirements and software installation: email us at mixomics[at]math.univ-toulouse.fr

12-14 Sept 2016, Toulouse, FR (COST)

Our workshop in Toulouse (3-day) was sponsored by EU COST Action “The quest for tolerant varieties: phenotyping at plant and cellular level (FA1306). and organised by GenoToul Biostat platform, Laboratory of Plant-microbe Interactions (LIPM) and Plant Science Research Laboratory (LRSV). We trained and coached 26 participants and had a great time during the third day (‘byo’ data) and the ice breaking gala dinner!

 

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Participants, organisers and tutors
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Looking very studious! We were hosted by the LIPM lab, INRA Auzeville Toulouse

Some feedback from our participants:

Overall I did enjoy the workshop, it was one of the most interesting and well put together that I have attended. Thank you very much.

The tutorials on the website are excellent for training.

It was a very good mixture of theory and practice to directly try out the methods. Also there were many experts who where available for questions. The presentations were quite clear to me as well as the course material and the provided scripts.

‘[Day 3] was useful, because it allows to check if we have well understood the use of each analysis, and bring our own data allows to make these analysis more concrete.’

[…] I could discuss with some other participants with similar experimental design and see how they think [they can] apply mixOmics

 

Data for Day 3 available:

Draught response in sunflower data with Get_started script (knitr format, open the .Rmd file with RStudio), with slides from David.

Some useful references discussed during the workshop:

Liu et al 2015: we used Principal Component Curves (a variant of PCA, but where you fit a curve, and where you need a ‘reference’ group) to quantify pathway regulation of Homologous Recombination in breast cancer.

Singh et al. 2016 (bioRxiv): the asthma study (#2) summarised some of the omics data sets into gene modules to quantify pathways before the integration step. This is the DIABLO paper.

Straube et al 2015: the linear mixed model framework to reduce the dimension of time course data from (n x p x T) to (T x p), lmms is available on CRAN.

Straube et al 2016: Dynomics to detect delay between time course data. Submitted.

Rengel et al. 2012 paper fr the drought response in sunflower.

Wickham 2014: tidy data

 

Sept 12-14 Sept 2016, Toulouse, FR

Dear mixOmics users,

It is our pleasure to announce the following mixOmics 3-day workshop sponsored by EU COST Action “The quest for tolerant varieties: phenotyping at plant and cellular level (FA1306). More details in the pdf here. We do offer some travel grants for PhD students and early career researchers.

Organized by

 Dates:  Monday 12 September until Wednesday 14 September 2016 (3 full days)

Practical information: The course fee is 300 € for the academia and 600 € for the industry. It covers tuition, course material, coffee/tea, lunches and 1 diner downtown on Monday 12 September. Please note that no fee will be counted for 12 PhD students and/or early postdocs (up to 8 years after Ph.D) selected by COST Action FA1306, and their travel and living expenses will be take in charge up to 650 €.

Location: Toulouse, France

Maximum number of participants: 30

Deadline for application: 15 June 2016

Decision for attendee selection and grant allowance: 30 June 2016

Registration: 4 to 15 July 2016

Apply for this Summer School at: https://www.surveymonkey.com/r/FLSYJZP

In addition, send a CV to E Jamet (jamet [at] lrsv.ups-tlse.fr) and do not forget to mention if you want to apply for a grant.

Contact in Toulouse:  E Jamet, LRSV, jamet [at] lrsv.ups-tlse.fr

Good luck!

March 24-25 2016, Nantes, FR

This was our first workshop of the year!

‘many thanks for that great tutorial’, ‘excellent training, excellent teachers, excellent visual aids’

When : 24-25 March 2015

Where : Nantes

Institution : L’Ecole Nationale Vétérinaire, Agroalimentaire et de l’Alimentation Nantes-Atlantique (http://www.oniris-nantes.fr/)

Lab : Laboratoire d’Etude des Résidus et des Contaminants dans les aliments (http://www.oniris-nantes.fr/services/laberca/)

Teachers : Sébastien Déjean, François Bartolo (Toulouse-based team)

Sept 24-25 2015, Jouy-en-Josas, FR

Date: 24-25 September 2015, 9.30am – 5.30pm

Venue: INRA Jouy-en-Josas, Allée de Vilvert, 78352 Jouy-en-Josas, France

‘paper, pdf and slide great, excellent pedagogy‘

‘A lot of informations were brought and must be adapted on our complex data. Workshop was well organized and the speech was really clear even if some things were not easy to understand when we don’t know all the statistical terms. But Kim-Ahn was very available for more explanations. Thank you very much. A lot of new ideas for data treatments… :)‘

2015-09-27 21.11.05
Sorry no pictures from the workshop this time. All characters appearing in this Totoro puzzle are fictitious. Any resemblance to real workshop participants is purely coincidental.

 

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Sept 14-15 2015, Toulouse, FR

Date: 14-15 September 2015, 9am – 5pm

Venue: Salle 131 Bâtiment administratif, INRA Toulouse Auzeville, Chemin de Borde Rouge, 31326 Castanet Tolosan cedex

‘I discovered a lot of new methods and it gives me ideas for future analyses. The practical part of the course is particularly interesting (make it more concret).’

‘intervenants très disponibles pour discuter, et nous aider’

‘super bonne préparation’ ‘bonne articulation theorique et pratique’

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Sébastien (bottom left) explaining some mixOmics concepts

mixomics_Biostat

 

Aug 13-14 2015, Brisbane, AUS

Our first Brisbane workshop entitled ‘mixOmics: exploration and integration of ‘omics data‘ is taking place at the Translational Research Institute in sunny Brisbane, where the Lê Cao team is based. The workshop is sponsored by AGTA small grant scheme, QIAGEN and our institutes the University of Queensland Diamantina Institute (UQDI) and the Translational Research Institute (TRI).

The workshop will be mostly targeting postgraduate students, postdocs and researchers working in biology, bioinformatics, computational biology, with a basic knowledge in statistics and good R programming skills.

Dates: 13-14 August 2015

Time: 9am – 5pm

Venue: SparQ-eD Room 2011, level 2, Translational Research Institute, 37 Kent st, Woolloonggabba, Brisbane.

‘The case studies were very helpful in understanding the type of data each test can be used with.’

‘Loved it. Very well presented, course material very clear and will be a useful resource in the future. Thanks Kim-Anh!!‘

‘Very nicely and clearly explained. Particularly appreciated that we were given the R scripts, so that we could concentrate on concepts rather than scripting.‘

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‘Everyone very helpful. Thanks Benoit!! You are a legend!’
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‘Very well designed such that the concepts were presented and explained while the trickiness of the R code was helped enormously by being able to follow the downloaded scripts. The tutors were very helpful in interpreting what the code was doing.’
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‘I really enjoyed the workshop – I found it very informative and the analogies used to help explain some of the more difficult concepts were very helpful.’

mixomics seminar poster final

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