Version update 19.12.2016: What is new in Chipster 3.11

Summary: This version contains a new tool category Single cell RNA-seq, and it also contains some updates and improvements to existing tools.


Version update 22.11.2016: What is new in Chipster 3.10

Summary: All the reference genomes and many analysis packages have been updated. This version contains also new and improved functionality for RNA-seq data. In particular, stranded RNA-seq data is now better supported and there is also a manual page for stranded RNA-seq data.


Version update 23.5.2016: What is new in Chipster 3.9.0

Summary:This version mainly contains internal changes to the way how tool scripts are distributed on the server side.


Version update 4.5.2016: What is new in Chipster 3.8.1

Summary: This version contains a bug fix for the tool Differential expression using DESeq2.


Version update 22.3.2016: What is new in Chipster 3.8

Summary: This version contains improvements to several analysis tools.


Version update 14.1.2016: What is new in Chipster 3.7

Summary: This version enables users to save analysis sessions on the server side. Please note that this cloud session functionality is still at a beta version stage, meaning that it might have unexpected problems. Therefore we strongly advice you to save an extra copy of your session also locally.


Version update 2.10.2015: What is new in Chipster 3.6

Summary: Many NGS tools have been updated to new versions, and reference genomes have been updated to Ensembl version 81. New NGS tools have been added. The job manager component of Chipster server has been re-written in Java in order to get rid of random messaging errors, which caused problems for example when starting the Chipster client software.


Version update 10.7.2015: What is new in Chipster 3.5

Summary: Result files from several NGS analysis tools are automatically named according to the original sample name, saving you the hassle of renaming files. Data can be imported directly to Chipster server from a url.


Version update 20.4.2015: What is new in Chipster 3.4


Version update 12.3.2015: What is new in Chipster 3.3

Summary: This version brings a major improvement as you can close Chipster while an analysis job is running, and return to the same session later when the results are ready.


Version update 9.2.2015: What is new in Chipster 3.2


Version update 6.11.2014: What is new in Chipster 3.1

Summary: This version contains important improvements to the user interface, file transfers, and reference data.


Version update 13.8.2014: What is new in Chipster 3.0

Summary: This is a major update which contains improvements to the user interface functionality and looks. All the NGS analysis tools except variant annotation have been updated to use R3.0.2. Several new NGS analysis tools have been added, and many existing tools have been updated and improved. The virtual machine has been updated to use Ubuntu 12.04.


Version update 21.5.2014: What is new in Chipster 2.12.1

Small bug fix update.


Version update 13.5.2014: What is new in Chipster 2.12

This is a small update which includes a couple of bug fixes and a new genome added to some aligners.


Version update 7.4.2014: What is new in Chipster 2.11

This is a major update which combines v2.10 and v2.11. It provides 62 new analysis tools, the majority of which are in the brand new sequence analysis module. New tools have been added also in the NGS module, including the Dimont motif finding tools kindly contributed by Jan Grau (Martin Luther University Halle-Wittenberg). Microarray analysis tools have been migrated to use R3.0.2 and the Brainarray custom CDFs version 18, and some NGS command line tools have been updated to new versions. Many existing tools and visualizations have been improved. The Chipster client can now be launched with more memory if needed for visualization.


Version update 4.12.2013: What is new in Chipster 2.9

Chipster 2.9 contains many analysis tool updates and improvements to the genome browser. It also contains some new analysis tools and a tutorial for CNA-seq data analysis kindly contributed by Ilari Scheinin (VU University Medical Center Amsterdam). In order to made it easier for the developer community to integrate new analysis tools in Chipster, this new version provides a graphical tool editor environment and support for Python.


Version update 30.8.2013: What is new in Chipster 2.8

Chipster 2.8 contains many improvements to visualizations and some new analysis tools. It requires Java 1.7, and contains a fix to the file import problem that some Windows users experienced.


Version update 28.6.2013: What is new in Chipster 2.7

Chipster 2.7 contains important updates to microarray tools and a new NGS tool category Metagenomics, which consists of Mothur tools for investigating bacterial composition from 16 S rRNA data.


Version update 27.5.2013: What is new in Chipster 2.6

Chipster 2.6 contains important updates to microarray and NGS analysis tools and some new NGS tools.


Version update 11.4.2013: What is new in Chipster 2.5

Chipster 2.5 contains a lot of new analysis and visualization functionality for NGS data and improvements to some microarray analysis tools. The new NGS data analysis tools include the TagCleaner package, F-seq peak detection software, and a large number of CNA-seq analysis tools kindly contributed by Ilari Scheinin (VU University Medical Center Amsterdam).


Version update 4.2.2013: What is new in Chipster 2.4

Chipster 2.4 contains changes to the user interface and analysis functionality. New genomes have been added to several analysis tools and to the genome browser.


Version update 13.11.2012: What is new in Chipster 2.3

Chipster 2.3 contains changes to the user interface and analysis functionality. NGS alignment tool Bowtie2 has been added, and changes have been made to existing alignment tools. Sheep genome oar3.1 has been added to alignment tools and genome browser. Support for some Agilent and Illumina microarrays has been added.


Version update 27.9.2012: What is new in Chipster 2.2.0

Chipster 2.2.0 contains a new tool category Variants with tools for analyzing VCF files. Visualization of these files is supported already (see the 12.9.2012 release notes). There are also new tools for RNA-seq analysis, and many tools have been updated to use Ensembl v68 annotations. The full list of NGS analysis tools is available here.


Version update 12.9.2012: What is new in Chipster 2.1.0

Chipster 2.1.0 contains major improvements in the genome browser and important new NGS data analysis functionality (see below). The full list of NGS analysis tools is available here.


Version update 6.7.2012: What is new in Chipster 2.0.2

Chipster 2.0.2 contains new analysis tools for variant calling (SAMtools) and quality control, trimming and filtering of reads (PRINSEQ). The full list of NGS analysis tools is available here.


Version update 24.1.2012: What is new in Chipster 2.0

Chipster 2.0 contains a comprehensive collection of analysis tools for next generation sequencing (NGS) data. Visualization options now include a built-in genome browser, allowing you to view reads and results in their genomic context. Importantly, also the analysis session handling has been improved.


Version update 16.5.2011: What is new in Chipster 1.4.7


The main change is new R/Bioconductor and annotation packages: All the R/Bioconductor-based analysis tools have been updated and now run under R 2.12.1 and Bioconductor 2.7. Please note that while Chipster 1.4.7 is focused on microarray and proteomics data analysis, new tools for next generation sequencing data are constantly added to Chipster 2.0.

Version update 7.12.2010: What is new in Chipster 1.4.6


Version update 14.10.2010: What is new in Chipster 1.4.5


This release completes the aCGH analysis functionality in Chipster. The aCGH functionality, kindly contributed by Ilari Scheinin (University of Helsinki), has now passed the beta testing phase, and the tools also have their manual pages. Please note that as "beta testing" has been removed from the category name, the workflows created with the test version won't be functional.

Version update 20.4.2010: What is new in Chipster 1.4.4

Fixed the 3D scatter plot bug of Chipster 1.4.3

Version update 9.4.2010: What is new in Chipster 1.4.3


Version update 11.2.2010: What is new in Chipster 1.4.2


Version update 20.1.2010: What is new in Chipster 1.4.1


Version update 11.11.2009: What is new in Chipster 1.4.0


Version update 17.7.2009: What is new in Chipster 1.3.0


Version update 27.3.2009: What is new in Chipster 1.2.4


Version update 5.2.2009: What is new in Chipster 1.2.3


Version update 8.1.2009: What is new in Chipster 1.2.2


Version update 11.11.2008: What is new in Chipster 1.2.1


Version update 13.10.2008: What is new in Chipster 1.2.0

New analysis tools

Visualization news

Support for new array types

Possibility to save multiple analysis sessions (workspaces)

In order to continue your work later on, you have to save your analysis session (workspace). Saving the session will save all the datasets and their relationships. In Chipster 1.2, a session is packed into a single compressed file with an extension .cs (for Chipster Session). This file is saved on your computer, but you can also take it with and continue your work on another computer by copying the session file there. Session files also allow you to share your work with a colleague. Chipster 1.2 allows you to save multiple analysis sessions separately, and you can save the session files anywhere you like.

To save a session select File->Save session. A previously saved session can be loaded by selecting File->Open session. By default the current data is cleared before another session is loaded, but you can also combine sessions by selecting "Add to current session" from the session file dialog.

Note! Sessions are an extended version of the previous workspace system. If you have saved a workspace with an earlier Chipster version, you can open it by selecting File->Open workspace (session) saved with Chipster 1.1. Unlike the old workspace system, the new session system also allows you to create workflows from datasets that were loaded from a session and you can view all the details for them (including the source code) in the analysis history.

More flexible analysis workflow saving

Workflows allow you to automate your analysis steps, and also share analysis pipelines with collaborators. Workflow is a description of the analysis steps that you've run to the currently selected dataset. If you have run a workflow that you would like to reuse or perhaps share with a colleague, you should save it by selecting its starting point data set and choosing Workflow->Save starting from selected. In Chipster 1.2 you can save the workflow file anywhere you like. You can also change its name, but the ending has to be .bsh.

You can apply the same workflow to another normalized dataset by selecting Workflow->Open and run, or Workflow->Run recent (if you saved the workflow during the same analysis session or if it is located under nami-workfiles in the chipster-scripts -folder).

General improvements