This repository represents an index to the main projects I developed in the framework of my PhD thesis. I will try to keep updated links to the public repositories, and also, when necessary, a frozen copy of it at my last contribution.
Each project has its own license, but as a general advice note that THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
- The thesis book (I had to remove a non open access paper)
- The thesis defence
Gitools is a framework for analysis and visualization of multidimensional genomic data using interactive heat-maps. You will find some tutorials in the main site of the tool.
I started this project and was the main contributor until the version 1.5.x. Afterwards other members of the group continued adding new cool features and fixing bugs until now (2015) where the development still continues.
The source code can be accessed from the public repository here
My main contribution to the IntOGen projects and papers is for the management of the genomic data, its analysis, and making the results available for internal and external researchers.
- intogen-arrays
- intogen-mutations: Last contribution for v2.4.2 Public repository
- oncodriveFM: Last contribution for v0.7-dev Public repository
- wok: Public repository
- IntOGen: integration and data mining of multidimensional oncogenomic data PDF
- IntOGen-mutations identifies cancer drivers across tumor types
- Integrative Cancer Genomics (IntOGen) in Biomart
- BioMart Central Portal: an open database network for the biological community
I was working on a benchmark for the performance of several functional impact assessment algorithms, driver mutations identification tools and general purpose conservation scores.