Details Integrative Omics analysis platform

Genome data

  • Biopet Shiva (gonl-GRCh38) – Genome – Framework containing pipelines usable for a variety of Next Generation Sequencing analyses.

Transcriptome data

  • RNAseq_multi_method – Transcriptome – Snakemake pipeline capable of running multiple RNA-sequencing analyses (different combinations of mappers, expression quantification methods and variant callers) at once.
  • Decon2 – Transcriptome – Consists of two tools: Decon-cell for predicting cell count proportions using RNA sequencing expression data, and Decon-eQTL to use (predicted) cell count proportions, RNA sequencing expression data, and genotypes to deconvolute cell type specifc eQTL effects from bulk tissue RNA sequencing data.

Epigenome data

  • MethylAid – Epigenome – Bioconductor package to interactively perform quality control for Illumina DNA methylation arrays including very large scale-datasets*.
  • WBCC predictor – Epigenome – R package that predicts blood cell counts using genome-wide methylation or expression data using a built-in predictor or using a custom-made predictor by the user*.
  • Epityper – Epigenome – Set of R scripts facilitating design and processing of locus-especific DNA methylation measurements using the mass-spectrometry based methods*. 

Multiple data

  • OmicsPrint - Genome, Epigenome, Transcriptome – Bioconductor package to verify and correct data linkage and sample swaps in (multiple) genomics data*.
  • BACON - Genome, Epigenome, Transcriptome, Metabolome – Bioconductor package that corrects for inflation and bias of test statistics in large-scale association studies*.
  • BBMRIomics - Genome, Epigenome, Transcriptome, Metabolome – R package that facilitates BBMRI-omics downstream analysis that is available at the BBMRI BIOS virtual machine running at SURFsara HPC Cloud.
  • MWAS and TWAS computation using the BIOS Consortium based prediction - Transcriptome, Metabolome – Creates models predicting gene expression using local (cis) SNPs, and uses GWAS summary statistics to estimate the association between the local genetic component of gene expression and the phenotype used for GWAS*.