DATA ANALYSIS, INTEGRATION & STEWARDSHIP SERVICES

  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            
NWO logoThis research was (partially) funded by NWO, project 184.034.019