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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. |
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capice.molgeniscloud.org molgenis/vip molgenis/NGS_DNA VEP_custom_annotations |
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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") |
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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 |
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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. |
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Links to repositories, papers etc. |
Workflowhub |
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Workflowhub |
PMID: 31937552 |
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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 |
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Links to repositories, papers etc |
molgenis molgenis-emx2 FAIRDataCube |
fairgenomes FAIR_policies_website_v3.pdf github.com/Xomics |
fairgenomes |
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FAIR_policies_website_v3.pdf |
online library: ggn2.10023 |
docs.gcc.rug.nl/fender/ |
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Reproducible data analysis |
Github for versioned code, script and software managementa |
Ansible playbooks for software and tool deployment |
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Workflow management |
Nextflow |
KNIME |
Kimble |
Galaxy |
MOLGENIS Compute for large scale data and computational workflow management in a distributed execution environment |
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