New OncodriveFM release 0.3.2

Some time ago Abel wrote about how to identify cancer drivers from tumor somatic mutations, and presented OncodriveFM. Nuria also posted a nice poster explaining it together with TransFIC.
Initially, OncodriveFM was written by Abel as a Perl script and distributed through our web. Later on I had to implement the analysis workflows of IntOGen SM, which required to use it intensively. However,
we realized that the code of OncodriveFM could be significantly improved in terms of performance, as there is a part of the analysis that  may take quite a lot of time depending on the input data. This is why I decided to implement it again, starting from a prototype written by Abel, using Python. Read the rest of this entry »

Oncogenomics workshop: my slides on the analysis of Somatic Mutations in IntOGen

Last week I attended the Oncogenomics Workshop in Hinxton. This was a really interesting Workshop organized by the Industry program of the EBI. It addressed the issues of which data are becoming available and how to access them, how to best analyze the oncogenomics data and interpret them, and which are the challenges ahead in terms of translating these data and knowledge into therapeutic opportunities. I was invited to present IntOGen and I thought it would be of interest to some followers of our blog if I shared the slides of the talk.

  Read the rest of this entry »

New IntOGen Somatic Mutations Analysis version available

We are proud to announce the brand new version of the IntOGen Somatic Mutations Analysis (IntOGen SM) pipeline. We call it version 2.0.0 as it has been completely rewritten from scratch with a strong focus on quality, efficiency and scalability.

The IntOGen SM pipeline addresses the challenge of identifying which somatic mutations are important for the development of tumors. The input for the analysis is a list of somatic mutations detected in a cohort of tumors. Read the rest of this entry »