Tools




Software

DisGeNET

DisGeNET is a discovery platform containing one of the largest publicly available collections of genes and variants associated to human diseases. DisGeNET integrates data from expert curated repositories, GWAS catalogues, animal models and the scientific literature. DisGeNET data are homogeneously annotated with controlled vocabularies and community-driven ontologies. Additionally, several original metrics are provided to assist the prioritization of genotype-phenotype relationships. Developed by the Integrative Biomedical Informatics group, the current version (v5.0) contains 561,119 gene-disease associations (GDAs), between 17,074 genes and 20,370 diseases, disorders, traits, and clinical or abnormal human phenotypes, and 135,588 variant-disease associations (VDAs), between 83,002 SNPs and 9,169 diseases and phenotypes.

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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).

visit eTOXlab website

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.

visit adr-substantiation website

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

GUILD (Genes Underlying Inheritance Linked Disorders) is a framework built for the prioritization of disease candidate genes using a priori gene-disease associations and protein interactions. GUILD consists of implementations of 8 algorithms: NetScore, NetZcore, NetShort, NetCombo, fFlow, NetRank, NetWalk and NetProp. Developed by the Structural Bioinformatics group.

Visit GUILD website

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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