How to generate mutation distribution and frequency plots?
Let’s plot some mutations! Easy, right? For our next iteration of the IntOGen database, we wanted to add figures that represent the mutation distribution across the protein [...]
How to perform a hierarchical clustering using interactive heatmaps in Gitools
In the latest version of Gitools, version 2.1, we have improved the clustering of heatmaps. Here we explain in detail on how to perform and interpret the [...]
How to identify functional genetic variants in cancer genomes?
The possibility to rapidly and inexpensively sequence tumor genomes is opening important new avenues for cancer research. One of the main objectives when sequencing tumor genomes is [...]
Interactive heat-maps to explore biological data
Heat-maps are graphical representations of data where values in a matrix are represented following a color scale. This way of representing data has proven to be a [...]
List of tools to visualize multidimensional cancer genomics data
A while ago we published a review about multidimensional cancer genomics data visualization in Genome Medicine. There, we focused on effective and common visualization techniques for exploring oncogenomics [...]
Condel for prioritization of variants involved in hereditary diseases and transFIC for cancer
We have worked during the last years on assessing the functional impact of non-synonymous variants (nsSNVs). As a result, we have published two new approaches Condel and [...]
How to evaluate the performance of computational methods to identify driver mutations?
We have recently published transFIC, a computational method to assess the functional impact of somatic cancer mutations (see this post). To evaluate the performance of transFIC we [...]
How to identify cancer drivers from tumor somatic mutations?
I have recently seen several presentations by groups that systematically explore alterations in cancer genomes that deliver the same message. One of the main challenges [...]
Sample Level Enrichment Analysis (SLEA) Tutorial and Gitools 1.6.2
As you may have read in the last post, Günes and Nuria presented the Sample Level Enrichment Analysis (SLEA) as a methodology to analyse the transcription level [...]
Exploring the effect of cancer genomic alteration on expression with Gitools
Cancer cells often exhibit a change in number of copies of certain genomic regions when compared to normal cells (Copy Number Alterations: CNAs). Some of these CNAs [...]
