Tools




Software

DisGeNET

DisGeNET is a a public knowledge management platform on the genomics of disease that offers information on genes and genomic variants associated with human diseases, which is obtained by integrating more than a dozen public resources and the scientific literature. DisGeNET contains one of the most comprehensive collections of genes and variants associated with human diseases that is currently available. Developed by the Integrative Biomedical Informatics group, the current version (6.0) contains approximately 600,000 associations between more than 17,000 genes and 24,000 human diseases, focusing particularly on genetic alterations associated with disease: this version includes more than 117,000 genomic variants associated with 10,000 diseases. In addition, the phenotypic landscape covered by DisGeNET has been expanded to include the genomic basis of clinical manifestations of diseases, both signs and symptoms, as well as laboratory tests results.

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eTOXlab

eTOXlab is a flexible modeling framework. It was developed for supporting models predicting the biological properties of chemical compounds (e.g. QSAR models) in production environments. Developed by the PharmacoInformatics group, in the framework of the eTOX project (GA115002).

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ADAN

ADAN (Applicability Domain ANalysis) is a a novel method for assessing the reliability of drug property predictions obtained by in silico methods. The assessment provided by ADAN is based on the comparison of the query compound with the training set, using six diverse similarity criteria.  Developed by the PharmacoInformatics group.

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SmartAS

SmartAS is a pipeline oriented to finding interesting isoform switches between two conditions, with as many replicates as desired. Developed by the Computational RNA Biology group.

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ADRs Substantiation

This is a novel computational framework to aid in the collection and exploration of evidences that support the causal inference of adverse drug reactions (ADRs) detected by mining clinical records. This framework was implemented as publicly available tools integrating state-of-the-art bioinformatics methods for the analysis of drugs, targets, biological processes and clinical events. The availability of such tools for in silico experiments will facilitate research on the mechanisms that underlie ADR, contributing to the development of safer drugs. Developed by the Integrative Bioinformatics group.

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ProfileSeq

ProfileSeq is a computational method for the quantitative assessment of biological profiles to provide an exact, nonparametric probability that specific regions of the test profile have higher or lower signal densities than a control set. The method is applicable to high-throughput sequencing data (ChIP-Seq, GRO-Seq, CLIP-Seq, etc.) and to genome-based datasets (motifs, etc.). Developed by the Computational RNA Biology group.

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GUILD

GUILDify v2.0 is a Tool to Identify Molecular Networks Underlying Human Diseases. A web server for phenotypic characterization of genes through biological data integration and network-based prioritization algorithms. Towards the goal of extending our knowledge on the genetic elements underlying various phenotypes (including but not limited to disease phenotypes), we aim to use gene-phenotype associations in combination with the network-based prioritization methods. Developed by the Structural Bioinformatics group.

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SUPPA

Developed by the Computational RNA Biology group, SUPPA is a tool that generates different Alternative Splicing (AS) events and calculates the PSI ("Percentage Spliced In") value for each event exploiting the fast quantification of transcript abundances from multiple samples.

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PsyGeNET

Developed by the Integrative Biomedical Informatics group, PsyGeNET (Psychiatric disorders and Genes association NETwork) is a knowledge platform for the exploratory analysis of psychiatric diseases and their associated genes. PsyGeNET is composed of a database and a web interface supporting data search, visualization, filtering and sharing.

PsyGeNET website

PALO

Developed by the Evolutionary Genomics group, Protein ALignment Optimiser (PALO) is an algorithm for the selection of the best combination of protein isoforms among orthologous genes in the construction of a multiple alignment. You can easily upload your files from ENSEMBL and this tool will tell you which is the most suitable combination for you to align.

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