Tools

Tools, software and resources

Tools, software and databases we develop and maintain

PTMcode

Database for known and predicted functional associations between protein post-translational modifications (PTMs).

http://ptmcode.embl.de

Machine learning R code

https://github.com/pminguez/MachineLearning4UnbalancedData

Snow (Studying Networks in the Omic World)

Extracts the protein-protein interaction networks behind a list of genes/proteins (signature) and evaluates its robutness against same-size networks generated from random lists of genes/proteins.

http://babelomics.org

Babelomics

We are part of the consortium that develops Babelomics (http://babelomics.org), an on-line platform for an integral analysis of transcriptomic experiments, from raw data, normalization, differential expression, clustering, machine learning and other statistical analyses to the functional profiling using classical, gene set and network approaches.

more on ... https://github.com/TBLabFJD

We also contributed somehow to other tools (in some of their releases)

STRING

Protein-protein interaction networks.

https://string-db.org

OGEE (database of Online GEne Essentiality)

http://ogeedb.embl.de

Old tools and databases we developed or contributed to ..

Tissues Mining Tool

Finds tissues and tissue histologies in which two lists of genes display different distributions.

http://www.babelomics.org

MarmiteScan

Use chemical and disease related information to detect related blocks of genes in a gene list with associated values.

http://www.babelomics.org

Marmite

Finds differential distributions of bioentities extracted from PubMed between two groups of genes.

http://www.babelomics.org

AtEnsembl

The Arabidopsis thaliana Genome browser.

http://atensembl.arabidopsis.info