Exploring multiple cancer genomics alterations with Gitools.

Cancer genomics data that is produced creates multi-dimensional data sets. Gitools lets you browse all that data at once.

A typical cancer genomics project nowadays screens the cancer genome, epigenome and transcriptome of a cohort of patients and identifies various types of alterations: Copy Number changes, Somatic Mutations, Gene Expression changes and others. This is the case of projects framed within The Cancer Genome Atlas or the International Cancer Genomics Consortium, as well as many others. Each of these types of alterations is represented in different data formats and it remains a challenge to integrate them to get a unified view of the process of alterations that leads to tumorigenesis. In Gitools it is possible to explore and analyze multi-value matrices in the form of interactive heatmaps, making it possible to work with various data dimensions at once.  Read the rest of this entry »

Gitools 1.6.0 release

We are pleased to announce that as of today a new version of Gitools is available: Gitools 1.6.0.

The change from the 1.5.x to 1.6.x series promise new features, and so it is! In general, Gitools got polished to make it easier to work with multi-dimensional data. Check the list below to see what’s new

Usability:

  • Color scales can be saved and loaded!
  • Display options for cell value/color scale are kept: when you define the display options of a value those are saved, so that when you switch back to see that value again the display options are kept.

Data analysis:

  • New Analysis: Group Comparison (Mann-Whitney-Wilcoxon), to compare the distribution of values between two sets of columns or rows
  • New sorting method: Mutual exclusive sorting

Plus several bugfixes.

Expect some follow-up posts explaining some of the novelties in detail.