News

SNPassoc

Software
This package was built when I was working at Xavier Estivill’s lab at Center for Genomic Regulation and it is written in collaboration with Victor Moreno and his colleagues. The R package SNPassoc contains classes and methods to help the analysis of whole genome association studies. SNPassoc utilizes S4 classes and extends haplo.stats R package to facilitate haplotype analyses. The package is useful to carry out most common analysis when performing whole genome association studies. These analyses include descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models (either for quantitative or binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis). Permutation and related tests (sum statistic and truncated product) are also implemented. The package is available from…
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BRGE at the New Horizons for Early Life Exposome Research

News
Dr Juan R. Gonzanez, the PhD Student Carles Hernandez-Ferrer and Marta Vives-Usano have a presentation during the first day of the HELIX symposium "New Horizons for Early Life Exposome Research". Here you can find the program of the symposium. Their speeches were entitled: Dr Juan R. Gonzalez: "Human epigenome, transcriptome, metabolome and proteome variability explained bu the exposome" Carles Hernandez-Ferrer: "Molecular signatures time variability in HELIX panel paired-samples" Marta Vives-Usano: "Smoking and methylation"
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HELIX project on El Periódico de Catalunya

News
​ Last Friday (October 27th, 2017), El Periódico de Catalunya came to ISGlobal to cover the HELIX Project that is being carried out in collaboration with many European research centres. Fortunately, the article was published two days before the symposium HELIX and ISGlobal are organizing for next Monday and Tuesday (New Horizons for Early Life Exposome Research) in Barcelona. The links to the Spanish and Catalan articles follow: ES CAT ​
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We were at the International Workshop Environmental Omics Integration & Modeling

News
​ Last Friday, our group leader Dr Juan R. Gonzalez and our colleagues Carles Hernandez-Ferrer and Marta Vives-Usano were at "International Workshop EnvironmEntal Omics Integration & Modeling" (CosmoCaixa, Barcelona, October 18-20). The aim of the workshop was to review the state-of-the-art of the high-throughput analytical methods, data integration and modelling in Environmental Omics and Toxicology. Here you can find the program of the event. The talks given by or group mebers were: Dr Juan R. Gonzalez: "MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integratio" Carles Hernandez-Ferrer: "rexposome: a bioinformatic tool for characterizing multiple environmental factors and its association with different omics biomarkers and disease" Meanwhile, Marta Vives-Usano was presenting the poster "The Human Early Life Exposome (HELIX) Project: Molecular Mechanisms"
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rexposome

Software
rexposome is an R package for exposome characterization and exposome-outcome test association. It was developed by Carles Hernandez-Ferrer as part of its PhD project and used in the analysis performed in HELIX Project. It depends in a series of third party R packages to provide: A basic pipeline for missing-data imputation in exposome, include the imputation of values under limit of detection. A series of functions to describe and characterize the exposome, including PCA in exposures and samples space, correlation between exposures and clustering of samples through exposure levels. Two different approaches to test the association exposome-diseasom in terms of Exposome-Wide Association Studies (ExWAS and mExWAS). The package can be found at GitHub and at Bioconductor: GitHub: rexposome Bioconductor: rexposome We are writing an article about the exposome pipeline analysis,…
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CTDquerier

Software
The *Comparative Toxicogenomics Database* is a public resource for toxicogenomic information manually curated from the peer-reviewed scientific literature about chemicals, gene and health outcomes interactions. It includes more than 30.5 million toxicogenomic connections. The `CTDquerier` package allows to retrieve CTD data into R environment to be used in CRNA or Bioconductor downstream analysis. The package can be bound at **GitHub**: * **GitHub**: [`CTDquerier`](https://github.com/isglobal-brge/CTDquerier) We have submitted an article about `CTDquerier` (sent: July 4th, 201): > **Carles Hernandez-Ferrer, Juan R. Gonzalez; CTDquerier: a tool for enrichment analysis in genetic and toxicological studies using CTD; Bioinformatics*
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omicRexposome

Software
This R package is built to extend the capabilities of the R package rexposome and to allow to find exposome molecular signatures. This is archived by implementing a limma wrapper that works with ExposomeSet objects. This is a work of the PhD project of Carles Hernandez-Ferrer. The package can be found at GitHub and at Bioconductor: GitHub: omicRexposome Bioconductor: omicRexposome We are writing an article about the exposome pipeline analysis, which is joint with rexposome package: Carles Hernandez-Ferrer, ... Juan R. Gonzalez; Comprehensive analysis of the exposome, exposomehealth associations and omics intermediates; XXXXXX
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MAD (Mosaic Alteration Detector)

Software
This is a joint work with Benjamin Rodriguez-Santiago (qGenomics) and Luis Pérez-Jurado (UPF). MAD is a software tool to detect mosaic events from SNP arrays using BAF and LRR values. The algorithm is based on a segmentation procedure which uses the main features of GADA (and R package to detect CNVs). To install MAD, start R and enter: [generic] source("http://www.creal.cat/media/upload/arxius/jr/CREAL_install/install.R") creal.install("mad") [/generic] The methodological paper has been accepted in BMC Bioinformatics and can be found here. An example about how to use the software is described in the vignette. The algorithm has been used to discover mosaic alterations in a large collaborative study: > *Jacobs KB, Yeager M, Zhou W, ... Gonzalez JR, ... Rothman N, Pérez-Jurado LA, Chanock SJ. Detectable clonal mosaicism and its relationship to aging and cancer.…
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inveRsion

Software
`inveRsion` is an R package for the detection of genetic inversions using SNP-array data. This is a joint collaboration with Alejandro Caceres (ISGlobal) and Suzanne Sindi (Center for Computational Molecular Biology, Brown University). `inveRsion` is available at Bioconductor, and a manuscript is published at BMC Bioinformatics: > *Cáceres A, Sindi SS, Raphael BJ, Cáceres M, González JR. Identification of polymorphic inversions from genotypes. BMC Bioinformatics. 2012 Feb 9;13:28.* Our aim is to use SNP-array data of large cohorts, for which phenotype information has been collected, to assess the association of inversions with disease. We also intent to use the tool to assist in the mapping of human inversions; a project headed by Mario Caceres (Universitat Autonoma de Barcelona). * **Bioconductor**: [`inveRsion`](http://bioconductor.org/packages/release/bioc/html/inveRsion.html)
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tweeDEseq

Software
`tweeDEseq` is an R package for analyzing RNAseq count data. It implements Poisson-Tweedie family of distributions to model count data distribution. This family includes Poisson and Negative Bionomial as particular cases. The testPT test is used to detect genes that are deferentially expressed (DE). The methods are described in the manuscript published at BMC Bioinformatics: > *Esnaola M, Puig P, Gonzalez D, Castelo R, Gonzalez JR. A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments. BMC Bioinformatics 2013, 14:254.* The manuscript illustrates the performance of our proposed method using a real RNA-seq data set comprising 69 Nigerian. We have created an experimental data pacakge (tweeDEseqCountData) that is available at Bioconductor. `tweeDEseq` is available from Bioconductor: * **Bioconductor**: [`tweeDEseq`](http://bioconductor.org/packages/release/bioc/html/tweeDEseq.html)
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