Difference: MultiOmicsWorkshop (1 vs. 7)

Revision 7
23 Nov 2017 - Main.PerryMoerland
Line: 1 to 1
 
<--  
-->
Line: 32 to 32
 

Time Type Subject Teacher Material
9.00-9.45 Lecture Weighted gene co-expression network analysis (WGCNA) Perry Moerland (AMC) Slides
Changed:
<
<
9.45-10.30 Hands-on WGCNA Perry Moerland & Koos Zwinderman Exercises (Rmd) Exercises (html) Answers (Rmd) Answers (html)
10.30-11.15 Lecture Sparse canonical correlation analysis (CCA) Koos Zwinderman (AMC)  
11.15-12.00 Hands-on Sparse CCA Perry Moerland & Koos Zwinderman  
>
>
9.45-10.30 Hands-on WGCNA Perry Moerland & Koos Zwinderman Lab (Rmd) Lab (html) Answers (Rmd) Answers (html)
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
 
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  
Revision 6
23 Nov 2017 - Main.PerryMoerland
Line: 1 to 1
 

Multi-omics analysis - Workshop

Line: 31 to 31
 
  • Location: Academic Medical Center, room: Costerzaal G0-209 (directions)

Time Type Subject Teacher Material
Changed:
<
<
9.00-9.45 Lecture Weighted gene co-expression analysis (WGCNA) Perry Moerland (AMC)  
9.45-10.30 Hands-on WGCNA Perry Moerland & Koos Zwinderman  
>
>
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 Exercises (Rmd) Exercises (html) Answers (Rmd) Answers (html)
 
10.30-11.15 Lecture Sparse canonical correlation analysis (CCA) Koos Zwinderman (AMC)  
11.15-12.00 Hands-on Sparse CCA Perry Moerland & Koos Zwinderman  
12.00-12.45 Lunch      
Changed:
<
<
12.45 - 15.45 Lecture and hands-on Network modeling for high-dimensional omics data Wessel van Wieringen (VU/VUmc) & Carel Peeters (VUmc)  
>
>
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  
Revision 5
20 Nov 2017 - Main.PerryMoerland
Line: 1 to 1
 
<--  
-->
Line: 13 to 13
 

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.
Added:
>
>
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:
Revision 4
18 Nov 2017 - Main.PerryMoerland
Line: 1 to 1
 
<--  
-->
Line: 9 to 9
 

Scope

Changed:
<
<
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 a lecture followed by a hands-on session, during which participants will get a better feel for the methods by practising on their own laptops.
>
>
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.
Revision 3
17 Nov 2017 - Main.PerryMoerland
Line: 1 to 1
 
<--  
-->
Line: 13 to 13
 

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.
Added:
>
>

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
Changed:
<
<
  • Location: Academic Medical Center, room Costerzaal G0-209 (directions)
>
>
  • Location: Academic Medical Center, room: Costerzaal G0-209 (directions)
 

Time Type Subject Teacher Material
9.00-9.45 Lecture Weighted gene co-expression analysis (WGCNA) Perry Moerland (AMC)  
Changed:
<
<
9.45-10.30 Lecture Sparse canonical correlation analysis (CCA) Koos Zwinderman (AMC)  
10.30-12.00 Hands-on WGCNA and sparse CCA Perry Moerland & Koos Zwinderman  
>
>
9.45-10.30 Hands-on WGCNA Perry Moerland & Koos Zwinderman  
10.30-11.15 Lecture Sparse canonical correlation analysis (CCA) Koos Zwinderman (AMC)  
11.15-12.00 Hands-on Sparse CCA Perry Moerland & Koos Zwinderman  
 
12.00-12.45 Lunch      
Changed:
<
<
12.45 - 14.15 Lecture Methods for network reconstruction using omics data Wessel van Wieringen (VU/VUmc) & Carel Peeters (VUmc)  
14.15 - 15.45 Hands-on Methods for network reconstruction using omics data Wessel van Wieringen & Carel Peeters  
>
>
12.45 - 15.45 Lecture and hands-on Network modeling for high-dimensional omics data Wessel van Wieringen (VU/VUmc) & Carel Peeters (VUmc)  
 
16.00 - 17.00 Lecture Open, reproducible machine learning research Joaquin Vanschoren  
Changed:
<
<

Software installation instructions

The hands-on sessions are based on R. You are strongly advised to install the most recent versions of R and RStudio on your laptop:
  • 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")) 
>
>
 

- PerryMoerland - 09 Nov 2017
Revision 2
10 Nov 2017 - Main.PerryMoerland
Line: 1 to 1
 
<--  
-->
Line: 27 to 27
 
14.15 - 15.45 Hands-on Methods for network reconstruction using omics data Wessel van Wieringen & Carel Peeters  
16.00 - 17.00 Lecture Open, reproducible machine learning research Joaquin Vanschoren  
Changed:
<
<

Installation instructions

The hands-on sessions are based on R. You are strongly advised to install the most recent versions of R and RStudio installed on your laptop:
>
>

Software installation instructions

The hands-on sessions are based on R. You are strongly advised to install the most recent versions of R and RStudio on your laptop:
 
Changed:
<
<
  • Then install the following R packages from the prompt:
>
>
  • Install the following R packages (and their dependencies):
 
source("http://bioconductor.org/biocLite.R") 
biocLite(c("WGCNA", "mixOmics")) 
 
This site is powered by FoswikiCopyright © by the contributing authors. All material on this collaboration platform is the property of the contributing authors.
Ideas, requests, problems regarding Foswiki? Send feedback