Application

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.		capice.molgeniscloud.org molgenis/vip molgenis/NGS_DNA VEP_custom_annotations		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	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 molgenis-emx2 FAIRDataCube	fairgenomes FAIR_policies_website_v3.pdf github.com/Xomics	fairgenomes		FAIR_policies_website_v3.pdf	online library: ggn2.10023	docs.gcc.rug.nl/fender/
	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 (www.researchenvironment.org) for secure, collaborative, cloud-based analyses	Local High Performance Computing clusters