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Wanted: Bachelor or Master (bio)-informatics student for small or large project.

 

Improving and extending MethylAid

 

MethylAid: visual and interactive quality control of large Illumina 450k datasets

Maarten van Iterson

m.van_iterson@lumc.nl

MethylAid was developed to serve the need for an efficient and interactive tool for quality control of large-scale epigenome-wide association studies performed on the Illumina Human 450k array.

MethylAid is an R/BioConductor package that uses shiny (http://shiny.rstudio.com) to generate the interactive web application and it contains several parallel programming solutions for fast summarization.

Since the first release version we got several requests for improving and extending the functionalities of MethylAid. There are several projects possible to add one or more of the extensions:

  1. Interactive graphics: The plots generated by MethylAid are linked and partly interactive we would like to extend these capabilities e.g. using javascript libraries like d3.
  2. Report generation: We got a request from the industry to automatically generate a report from the web application. This requires writing markdown template files and use literate-programming using the R packages: rmarkdown (http://rmarkdown.rstudio.com) and knitr (http://yihui.name/knitr/).
  3. Apart for these slightly larger projects there are several smaller additions that we would like to make: generate and      visualize a background data set, explore ways to deploy the application using e.g. shiny server (https://www.shinyapps.io/), improve the web application layout and documentation and add additional data subsetting      functionalities.

 

For this project we are looking for a bachelor’s or master’s student (bio)-informatics.

Minimal requirements: Basic knowledge of R programming language.

If interested please contact Maarten van Iterson: m.van_iterson@lumc.nl

Paper: bioinformatics.oxfordjournals.org/content/30/23/3435

Software: www.bioconductor.org/packages/3.0/bioc/html/MethylAid.html

Demo: shiny.bioexp.nl/MethylAid

 

contact

Maarten van Iterson

p     +31 (0) 71 526 9745
w    www.molepi.nl     
e    m.van_iterson@lumc.nl