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Data analysis, integration & stewardship services

The main area of expertise of the data facilities, that are part of the X-omics research infrastructure, consists of integration of X-omics data, FAIRification of -omics data, reproducible data analysis and workflow management. The services are described below.

Upstream data analysis

  • Diagnostics quality variant calling
  • Long read analysis and optical mapping
  • Differential expression analysis
  • Quantitative, LC-MS & phospho-proteomics analysis
  • Quantitative Metabolomics analysis
  • UntargetedMetabolomicsanalysis
  • Methylation analysis
  • Microbiomics analysis
  • Lipidomics analysis

Downstream data analysis

  • Somatic variant analysis and structural variations
  • RNA Isoform & splicing analysis
  • Pathway analysis for RNA-Seq, Methylation and Untargeted Metabolomics
  • Next-generation metabolic screening
  • Metabolite set enrichment analysis
  • Genotype linkage to phenotype and rare diseases
  • FAIRification, Data Ontology support and Text mining

Multi-omics data analysis & integration

  • Proteogenomics combining Proteomics with DNA, RNA or Long reads
  • Pathway and gene network integration
  • Statistical integration of multi-omics data

All services mentioned above are custom services.
Please contact our helpdesk for a quote with turnaround times and prices based on your research question.

  Expertise Associated pipelines / workflows
  Analysis of genomics, transcriptomics, proteomics and metabolomics data Whole exome and whole genome analysis pipelines Microbiome analysis pipeline RNA-seq analysis pipelines Proteomics analysis pipelines Metabolomics analysis pipelines Glycoproteomics analyis pipelines Analysis and integration of lipidomics, proteomics, and transcriptomics data
Links to repositories, papers etc.
molgenis/NGS_RNA Threshold Avoiding Proteomics Pipeline (TAPP; molgenis/NGS_RNA PMID: 21879761); (PASTAQ PMID: 34355890") metabolite set enrichment analysis method (PMID: 35546254); ( Next Generation Metabolic Screening PMID: 34564390") GitHub - ndcn/omicser: The NDCN omics browser app for browsing and sharing general omics data.
PMID: 34859676
PMID: 34050187
PMID: 31808596
PMID: 28011752
PMID: 33483739
PMID: 35143212
PMID: 34680183
  Integration of X-omics data: statistical and knowledge-based integration Dimensionality reduction techniques Pathway and network-based integration Proteogenomics pipelines Accurate hypothesis testing for Gaussian Graphical Models Supervised analysis/ Predictive modeling General mass spectrometry data analysis.  
Links to repositories, papers etc. Workflowhub   Workflowhub PMID: 31937552        
  FAIRification of -omics data
FAIR Data Cube
Guidelines and tools for FAIR representation of clinical, sample, measurement, bioinformatics methods, and -omics data; Data Management Planning Machine-readable consents and conditions of use BBMRI Biobank and biosample catalogues Guidelines for and development of FAIR and reproducible data analysis workflows Phenotype to gene matching algorithms for Rare Disease patients Reproducible cloud computing on HPC environments for Rare Disease analysis  
Links to repositories, papers etc molgenis
fairgenomes   FAIR policies X-omics_v4.pdf online library: ggn2.10023  
  Reproducible data analysis Github for versioned code, script and software managementa Ansible playbooks for software and tool deployment          
  Workflow management Nextflow KNIME Kimble Galaxy MOLGENIS Compute for large scale data and computational workflow management in a distributed execution environment    
  ICT Infrastructures
  Digital Research Environment ( for secure, collaborative, cloud-based analyses Local High Performance Computing clusters