• 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

Download Now! Gitools 1.5.9 (26.26 MB)

• 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

Download Now! Gitools 1.5.8 (26.25 MB)

• 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

Download Now! Gitools 1.5.7 (26.28 MB)

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

Download Now! Gitools 1.5.6 (26.25 MB)

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

Download Now! Gitools 1.5.5 (22.39 MB)

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

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

Download Now! Gitools 1.5.4 (22.36 MB)

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

Download Now! Gitools 1.5.3 (11.94 MB)

• Biomart filters
• Hierarchical and k-means clustering
• Oncodrive analysis from command line
• Heatmap editor bug fixes

Download Now! Gitools 1.5.2 (12.26 MB)

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.

Download Now! Gitools 1.5.1 (6.94 MB)

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