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.
  1. New NGS analysis tools
  2. Updated NGS analysis tools
  3. New microarray analysis tools
  4. Updated microarray analysis tools

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.
  1. NGS functionality. The following analysis packages and several R-based tools are now available under the NGS tab in the Analysis tool panel. For more information about the individual tools, please see the NGS tool manual.
  2. Built-in genome browser

  3. Improved analysis session handling


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.
  1. New analysis tools

  2. Changes to analysis tools

  3. Obsolete analysis tools

  4. Visualization changes


Version update 7.12.2010: What is new in Chipster 1.4.6

  1. New analysis tools

  2. Changes to analysis tools

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.
  1. New analysis tools

  2. Changes to analysis tools

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

  1. New analysis tools
    This release completes the miRNA analysis functionality in Chipster and also includes a whole new set of tools for aCGH data. The aCGH functionality, kindly contributed by Ilari Scheinin (University of Helsinki) also allows to integrate aCGH data with expression data.
  2. Changes to analysis tools
  3. Changes to visualizations

Version update 11.2.2010: What is new in Chipster 1.4.2

  1. New functionality
  2. Changes to analysis tools
  3. Changes to visualizations

Version update 20.1.2010: What is new in Chipster 1.4.1

  1. New analysis tools
  2. Changes to analysis tools
  3. Visualization news:

Version update 11.11.2009: What is new in Chipster 1.4.0

  1. New R/Bioconductor version, updated annotation packages
    All the analysis tool scripts have been updated to use R 2.9. Consequently the annotation and pathway tools have been updated to use annotation packages in the .db -format. The following versions of the annotation packages are currently in use:
  2. New analysis tools
  3. Changes to analysis tools
  4. Visualization news:
  5. Import tool can be used to convert decimal separator (e.g. from comma to dot) in the files to be imported to Chipster
  6. Bug fixes to session and workflow functionality.

Version update 17.7.2009: What is new in Chipster 1.3.0

  1. Support for new chip types
  2. New analysis tools
  3. Visualization news:

Version update 27.3.2009: What is new in Chipster 1.2.4

  1. New analysis tools
  2. Support for new chip types
  3. Solved problems

Version update 5.2.2009: What is new in Chipster 1.2.3

  1. Chipster is updated automatically also when you start it using the desktop icon (but we still recommend you to launch it from the web page, as this way you can read the latest announcements as well)
  2. Normalization/ Affymetrix exon arrays: Updated the script to use Bioconductor 2.2 in order to overcome the affyio bug.

Version update 8.1.2009: What is new in Chipster 1.2.2

  1. New analysis tools
  2. Changes to analysis tools
  3. Visualization news:

Version update 11.11.2008: What is new in Chipster 1.2.1

  1. New functionality and visualization:
  2. Changes to analysis tools
  3. Annotation support for new chip types:

Version update 13.10.2008: What is new in Chipster 1.2.0

  1. New analysis tools
  2. Visualization news:
  3. Support for new array types
  4. Possibility to save multiple analysis sessions (workspaces)
  5. More flexible analysis workflow saving
  6. General improvements

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