Multi-omics analysis - Workshop

Scope

Omics technology has revolutionized molecular approaches towards understanding (human) disease. Unfortunately, data stemming from various omics platforms, such as genomics, transcriptomics, proteomics, and metabolomics, tend to be analyzed separately. To fully harness the power of these big data, a simultaneous analysis is required. In this workshop front-line methods for multi-omics data will be explored. This will involve two sessions: Each session will involve lectures and hands-on sessions, during which participants will get a better feel for the methods by practising on their own laptops.

The day will close with a talk by Joaquin Vanschoren (Eindhoven University of Technology) on Open, Reproducible Machine Learning Research. Joaquin's research focusses on the progressive automation of machine learning. He has founded OpenML.org, a platform for networked machine learning research used by researchers all over the world.

The workshop is part of a 2-day event with a symposium on Friday, November 24, 2017.

Software installation instructions

You have to bring your own laptop (and power cord!). Please install the most recent versions of R, RStudio, and the packages mentioned below before the workshop:
  • Download and install R v3.4.2
  • Download and install RStudio
  • Install the following R packages (and their dependencies):
source("http://bioconductor.org/biocLite.R") 
biocLite(c("WGCNA","mixOmics","rags2ridges","ragt2ridges","sigaR","longitudinal","SparseTSCGM"))

Schedule

  • Date: November 23, 2017
  • Location: Academic Medical Center, room: Costerzaal G0-209 (directions)

Time Type SubjectSorted ascending Teacher Material
12.00-12.45 Lunch      
12.45 - 15.45 Lecture and hands-on Network modeling for high-dimensional omics data Wessel van Wieringen (VU/VUmc) & Carel Peeters (VUmc) Outline Part 1 Part 2
16.00 - 17.00 Lecture Open, reproducible machine learning research Joaquin Vanschoren  
10.30-11.15 Lecture Sparse canonical correlation analysis (CCA) Koos Zwinderman (AMC) Slides
11.15-12.00 Hands-on Sparse CCA Perry Moerland & Koos Zwinderman See above
9.00-9.45 Lecture Weighted gene co-expression network analysis (WGCNA) Perry Moerland (AMC) Slides
9.45-10.30 Hands-on WGCNA Perry Moerland & Koos Zwinderman Lab (Rmd) Lab (html) Answers (Rmd) Answers (html)

- PerryMoerland - 09 Nov 2017
Topic revision: r7 - 23 Nov 2017, PerryMoerland
 

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