.

SOFTWARE & DATA

Epigenetics Software

PMA

Pathway Methylation Analysis (PMA) is an R package designed to test for the presence of differential methylation at the pathway level using permutation and filtering for reduntant CpG signals. The method has been developed for data generated by the Illumina 450K array although it can be easily adapted to the recent Illumina EPIC arrays or to any other methylation analysis platform.

Genetics Software

GStream

GStream is a method that combines SNP and CNV genotyping with unprecedented accuracy. This new method outperforms previous well-established SNP- and CNV-genotyping software for the Illumina platform.

2chi2

2chi2 is a new and highly powerful methodology to detect gene-gene interactions (epistasis) for binary traits . 2chi2 is also extremely fast computatinally, allowing the possibility to conduct Genomewide Analysis of Epistasis on large datasets. For this objective we provide an MPI parallelized version of the software.

CNStream

CNStream is a method for whole-genome Copy Number Variant discovery and genotyping , using Illumina Beadchip arrays. CNstream has been implemented as an R statistical software package that can work directly from raw intensity files generated from Illumina GWAS projects.

Metabolomics Software

FOCUS

FOCUS is a complete workflow Nuclear Magnetic Resonance (NMR) data processing that provides efficient methodological advances both on peak alignment and metabolite identification.

AStream

AStream is an R-statistical software package for the curation and identification of feature peaks extracted from liquid chromatography mass spectrometry (LC/MS) metabolomics data . AStream provides a reliable summarization of LC/MS metabolomic data, notably reducing curation time and increasing consistency of results.

For questions regarding these software tools contact bioinformatics@urr.cat.

Published Data

Aterido A, Julià A, Ferrandiz C, et al. Genome-wide pathway analysis identifies new genetic pathways associated with psoriasis. Journal of Investigative Dermatology 2015 (accepted for publication).

Julià A, Domèch E, Chaparro M, et al. A Genome-wide Association Study Identifies a Novel Locus at 6q11.2 Associated with Ulcerative Colitis (accepted for publication).Human Molecular Genetics 2014. PubMed

Julià A, Ballina J, Cañete J, et al. Genome-wide association study of rheumatoid arthritis in the Spanish population: KLF12 as a risk locus for rheumatoid arthritis susceptibility. Arthritis Rheum 2008;58(8):2275-2286. PubMed

Funding Agency:

Smiley face