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@Xomics The Netherlands X-omics Initiative

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    23 repositories

    • iPSC-data-analysis

      Public
      Multi-omics analysis of iPSC-derived neurons
      R
      •0•0•0•0•Updated May 20, 2026May 20, 2026

    • FAIRDS

      Public
      FAIRDataStation metadata and templates for x-omics projects
      1•0•0•0•Updated Apr 3, 2026Apr 3, 2026

    • Docker_containers

      Public
      Collection of Docker containers that are used in X-omics workflows
      Dockerfile
      •0•0•0•0•Updated Feb 13, 2026Feb 13, 2026

    • FAIRDataCube

      Public
      Design and implementation of FAIR Data Cube
      Jupyter Notebook
      •
      MIT License
      •6•12•0•4•Updated Jun 2, 2025Jun 2, 2025

    • TWOCdemonstrator

      Public
      X-omics TWOC demonstrator
      Python
      •
      MIT License
      •1•3•2•0•Updated Oct 18, 2024Oct 18, 2024

    • ACTIONdemonstrator_workflow

      Public
      X-omics ACTION demonstrator multi-omics analysis workflow
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Nov 24, 2023Nov 24, 2023

    • ISA-ACTION-Template

      Public
      Template for the creation of ISA-Tab files for the ACTION demonstrator project (with fake IDs)
      Jupyter Notebook
      •
      Apache License 2.0
      •0•2•0•0•Updated Oct 25, 2023Oct 25, 2023

    • r-base-phenotypes

      Public
      Docker container behavioral data pre-processing in R
      Dockerfile
      •0•0•0•0•Updated Oct 24, 2023Oct 24, 2023

    • r-base-epigenomics-pre

      Public
      Docker container epigenomics data pre-processing in R
      Dockerfile
      •0•0•0•0•Updated Oct 24, 2023Oct 24, 2023

    • mofa2

      Public
      Docker container for running Multi-Omics Factor Analysis (MOFA) in R
      Dockerfile
      •0•0•0•0•Updated Oct 24, 2023Oct 24, 2023

    • miniconda-snf

      Public
      Docker container for running Similarity Network Fusion (SNF) in Python
      Dockerfile
      •0•0•0•0•Updated Oct 24, 2023Oct 24, 2023

    • r-base-analysis

      Public
      Docker container for running basic unsuperivised method in R
      Dockerfile
      •0•0•0•0•Updated Oct 23, 2023Oct 23, 2023

    • ISA-templates-multi-omics

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Oct 4, 2023Oct 4, 2023

    • FAIRDataCube_cookbook

      Public
      Python
      •0•0•0•0•Updated Jun 8, 2023Jun 8, 2023

    • .github

      Public
      0•0•0•0•Updated Jun 7, 2023Jun 7, 2023

    • ACTIONdemonstrator_preprocessing

      Public
      Pre-processing workflow of the ACTIONdemonstrator
      R
      •0•0•0•0•Updated Jun 7, 2023Jun 7, 2023

    • Isatools_environment

      Public
      Computational environment to work with Isatools
      Jupyter Notebook
      •
      Apache License 2.0
      •1•1•0•0•Updated May 23, 2023May 23, 2023

    • omics_feature_mapping_examples

      Public
      HTML
      •
      Apache License 2.0
      •0•0•0•0•Updated Apr 26, 2023Apr 26, 2023

    • nf_modules

      Public
      Collection of nextflow modules that can be re-used
      Jupyter Notebook
      •0•0•0•0•Updated Nov 9, 2022Nov 9, 2022

    • Genomics_Metadata

      Public
      Shell
      •
      Apache License 2.0
      •4•0•0•0•Updated Jun 10, 2021Jun 10, 2021

    • MetabolomicsMeta-data

      Public
      0•1•0•0•Updated Feb 20, 2020Feb 20, 2020

    • DemonstratorUsecase

      Public
      Demonstrating Usecase
      0•0•0•0•Updated Feb 11, 2020Feb 11, 2020

    • ProteomicsMeta-data

      Public
      0•0•0•0•Updated Feb 6, 2020Feb 6, 2020
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