Chipster – open source data analysis platform

Chipster is a user-friendly analysis software for high-throughput data. It contains over 350 analysis tools for next generation sequencing (NGS), microarray, proteomics and sequence data. Users can save and share automatic analysis workflows, and visualize data interactively using a built-in genome browser and many other visualizations.

Chipster’s client software uses Java Web Start to install itself automatically, and it connects to computing servers for the actual analysis. Chipster is open source and the server environment is available as a virtual machine image free of charge. If you would like to use Chipster running on CSC’s server, you need a user account.

Upcoming Training Sessions:

  • 29.10.2015 RNA-seq data analysis, DPPS
  • 26.-27.10.2015 RNA-seq data analysis, Biomedicum
  • 29.9 and 5.10.2015 Variant analysis, Biomedicum
  • 18.9.2015 RNA-seq data analysis, Ljubjana

Video Tutorials:

Here we explain the use of edgeR in multivariate experiments in Chipster when studying differential expression from RNA-Seq data. This is the tool you want to use when you have several factors in y…


2:49 – Differential expression analysis tools for RNA-Seq

Here we briefly present the tools available in Chipster for differential expression analysis of RNA-Seq data.


4:00 – Using the “nested” option in multivariate edgeR

Here we demonstrate how you can use the “multivariate version” of edgeR -tool in Chipster to analyse your differential expression RNA-seq data, when you are doing comparisons both between and withi…

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