June 20th, 2011

Release 1.5.9

Bug fixes:

  • The GO and KEGG importers work fine now for all the types of identifiers
  • An exception when annotations don’t contain all the labels have been fixed
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Gitools 1.5.9 (26.26 MB)

June 10th, 2011

Release 1.5.8

Bug fixes:

  • The GO ontology importer has been adapted to the last changes of Ensembl release 62
  • The windows launcher has been finally fixed so it can be run with windows
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Gitools 1.5.8 (26.25 MB)

May 14th, 2011

Release 1.5.7

This release fixes two bugs:

  • Windows users are not able to launch it from the zip by clicking on gitools.bat
  • Filtering by labels doesn’t sort accordingly the filtered rows/columns
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Gitools 1.5.7 (26.28 MB)

March 25th, 2011

Release 1.5.6

This release implements many bug fixes and a brand new feature: colored labels and multiple headers for heatmaps.

Now it is possible to add many headers to heatmaps. At this time there are two type of headers: Text and colored labels.

Text labels allow to have identifiers and annotations in multiple columns, and colored labels show color bands depending on annotations of the rows/columns.

Users can report bugs or ask for new features or support at https://bg.upf.edu/forge/projects/gitools

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Gitools 1.5.6 (26.25 MB)

December 17th, 2010

Release 1.5.5

Previous release included a dedicated importer for Gene Ontology modules. It created a different module for each GO term with only the genes directly annotated for the GO term. In the version 1.5.5 we have modified the importer to take into account the hierarchy of dependencies between GO terms in a way that the genes associated with the module will be those directly annotated for the GO term plus the ones annotated for any of the GO term descendants.

Example:

Given the following GO tree and gene annotations

GO:001 –> GENE:001, GENE:002

+–GO:002 –> GENE:003

Previous release would generate 2 modules:

GO:001 with genes GENE:001, GENE:002

GO:002 with genes GENE:003

Release 1.5.5 would generate 2 modules as follows:

GO:001 with genes GENE:001, GENE:002, GENE:003

GO:002 with genes GENE:003

If any of you would still like to have the old way of importing GO terms available, let me know and we will considere having both options in the importer.

Users are able to report bugs or ask for new features or support at https://bg.upf.edu/forge/projects/gitools

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Gitools 1.5.5 (22.39 MB)

December 16th, 2010

Gitools goes Open Source

This last Friday we published the code of Gitools software under an open source license (Apache 2.0). We have made the source code available through the subversion repository and we allow users to report bugs and suggestions using the Redmine project management web application at https://bg.upf.edu/forge/projects/gitools.

More information at http://bg.upf.edu/blog/2010/12/gitools-goes-open-source/


November 5th, 2010

Release 1.5.4

New features and bug fixes:

  • Combination of p-values implemented
  • Improvements on details and analysis views
  • Html tables for related data and results depending on the heatmap selection
  • Better examples included and the posibility to execute analysis wizards with them automatically
  • gitools-convert command line tool to convert between formats
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Gitools 1.5.4 (22.36 MB)

June 4th, 2010

Release 1.5.3

New features and bug fixes:

  • Gitools can be runned directly from the web (thanks to Java Web Start)
  • Oncodrive and correlations wizards
  • General improvements when opening files
  • Help links on the welcome page
  • Downloading of some examples from the welcome page
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Gitools 1.5.3 (11.94 MB)

May 25th, 2010

Release 1.5.2

New features and bug fixes:

  • Biomart filters
  • Hierarchical and k-means clustering
  • Oncodrive analysis from command line
  • Heatmap editor bug fixes
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Gitools 1.5.2 (12.26 MB)

March 31st, 2010

Release 1.5.1

A new release of Gitools is available.

Apart from some bug fixes these are the most relevant new features:

  • Now it is possible to access to different releases of Ensemble using the Biomart import wizard.
  • Another new feature is the possibility to run correlations from a heatmap either for columns or rows, just open a heatmap and go to Analysis -> Correlation.
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Gitools 1.5.1 (6.94 MB)

March 21st, 2010

Release 1.5.0

We are proud to announce the new version of Gitools 1.5.0, it implements many improvements and new features like the ability to import data from IntOGen and Biomart.

You can download and give it a try:

Download Now!
Gitools 1.5.0 (5.84 MB)

To install it, uncompress the zip file and double click on bin/gitools if you are a Mac OS X or Linux user, if you are a Windows user then double click on bin/gitools.bat


March 12th, 2010

Release 1.4.10

This is the old version that we were using before releasing 1.5.

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Gitools 1.4.10 (2.31 MB)