We have started to distribute Gitools in the version 1.8.x. This latest version include important new features in terms of communication of Gitools with other tools (i.e. IGV, GenomeSpace, GSEA, excel). Now the user will get more flexibility for loading data in Gitools. These are the most important improvements in that aspect:
- Send matrices from IGV (Integrative Genomics Viewer) directly to Gitools
- Load matrices from GenomeSpace
- .GCT file support for matrix files (format used by GSEA).
- Import matrices from Excel data sheets
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New in Gitools 1.8.x: Support for loading data from Genome Space, importing from Excel and the .gct file format
GenomeSpace aims to be a platform that manages the researcher’s data and at the same time alleviates them from tedious tasks like converting data from and to different data formats. This approach holds a great promise to get standardizations for biological data and improved data transfer between different tools. We have enabled Gitools to log into GenomeSpace and load data. Tools that also connect to GenomeSpace are ArrayExpress, IGV, GenePattern, Cytoscape and more. See here for yourself.
IGV (Integrative Genomics Viewer)
Another great news is that the people at the Broad Institute have been working on a new feature for IGV which will let the user export loaded track data into .tdm matrix format and also load it directly in Gitools. For the latter, both Gitools and IGV need to be running so that they are able to communicate one with the other and transfer the data. Also note that sample information has to be loaded in order to let IGV know which tracks are from the same sample. This makes it possible for IGV to send matrices to Gitools that contain multidimensional genomics data as for example a matrix where each cell contains a value for expression, mutation and copy number variations for each sample and gene. As this is a new feature in IGV – and not in its definitive form – it is available through the early access versions which are preview versions presenting the features of the future releases. We see this as a great new feature that enables the user to work with two specialized and complementary visualization tools at once, which is enhanced by the link available in Gitools which navigates in IGV to a locus of interest.
Excel and .GCT
The .gct file format which is used by GSEA is now supported by Gitools for loading data to avoid the hassle of converting to .cdm. To the same end, Gitools can now import data directly from Excel data sheets. A wizard guides the user to choose which columns of the excel file correspond to the columns, rows and cells of the heatmap.
Gitools 1.7.0: the new features
Exploring multiple cancer genomics alterations with gitools
Visualizing mutually exclusive alteration patterns in cancer with gitools
Gitools published in plos one