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    28 repositories

    • Lifelines_NEXT

      Public
      Lifelines NEXT is a birth cohort designed to study the effects of intrinsic and extrinsic determinants on health and disease in a four-generation design. It is embedded within the Lifelines cohort study, a prospective three-generation population-based cohort study recording the health and health-related aspects of 167,729 individuals living in N…
      R
      •5•6•0•1•Updated Dec 20, 2024Dec 20, 2024

    • PhylogeneticAssociation

      Public
      Subspecies level association study.
      HTML
      •0•0•0•0•Updated Dec 17, 2024Dec 17, 2024

    • LLNEXT_pilot

      Public
      We studied the dynamics of the maternal gut virome during and after pregnancy, the infant gut virome during early life, with a particular focus on the transmission of viral strains from mothers to their infants.
      R
      •2•3•0•0•Updated Dec 12, 2024Dec 12, 2024

    • Somatic_mutations_IBD

      Public
      R
      •0•0•0•0•Updated Dec 4, 2024Dec 4, 2024

    • NCP_VLP_project

      Public
      This repository contains the scripts used during the data analysis for the paper “Negative control virome: characterization and decontamination in early-life studies”
      R
      •0•1•0•0•Updated Nov 13, 2024Nov 13, 2024

    • MicrobeRX

      Public
      MicrobeRX
      cheminformaticscomputational-biologymicrobiomedrug-designmetabolic-modelsgut-microbiomeenzymesmetabolite-identificationmetabolite-predictionmetabolite
      Python
      •
      GNU General Public License v3.0
      •2•9•0•0•Updated Nov 7, 2024Nov 7, 2024

    • CS_BABY_BIOME

      Public
      R
      •0•0•0•0•Updated Oct 18, 2024Oct 18, 2024

    • Groningen-Microbiome

      Public
      Microbiome Projects from the Department of Genetics and Department of Gastroenterology and Hepatology , University Medical Centre Groningen
      HTML
      •45•54•2•0•Updated Sep 19, 2024Sep 19, 2024

    • GMH_MGS_pipeline

      Public
      Groningen Microbiome Hub Metagenomic data analysis pipelines and scripts
      Python
      •
      Mozilla Public License 2.0
      •0•0•0•0•Updated Sep 10, 2024Sep 10, 2024

    • SNV_MWAS

      Public
      Analysis code for SNV-MWAS project
      R
      •
      MIT License
      •0•0•0•0•Updated Aug 26, 2024Aug 26, 2024

    • Small_intestine_IBD_virome

      Public
      Shell
      •0•0•0•0•Updated Aug 1, 2024Aug 1, 2024

    • 2024_Workshops_for_students

      Public
      Microbiome workshops for students
      R
      •0•0•0•0•Updated Jun 17, 2024Jun 17, 2024

    • MicrobeRX_DrugPredictions

      Public
      This repository includes the databases and analysis workflow for 1083 orally administrated drugs using MicrobeRX
      Python
      •
      GNU Affero General Public License v3.0
      •0•3•0•0•Updated Jun 12, 2024Jun 12, 2024

    • IBD_Drug_Response

      Public
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated May 21, 2024May 21, 2024

    • Lifelines_NEXT_milk_microbiota

      Public
      Research of mother milk and infant microbiome
      R
      •
      Other
      •0•0•0•0•Updated Apr 23, 2024Apr 23, 2024

    • Phip-Seq_LLD-IBD

      Public
      Scripts for data analysis of Phip-Seq (microbial and allergen libraries) in LLD and 1000IBD studies
      HTML
      •
      MIT License
      •1•0•0•0•Updated Jan 11, 2024Jan 11, 2024

    • MilkMethods2023

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated Nov 10, 2023Nov 10, 2023

    • SV_GWAS

      Public
      This repository contains the code used for SV-GWAS project
      R
      •5•6•0•0•Updated Oct 19, 2023Oct 19, 2023

    • SV_IBD

      Public
      R
      •0•0•0•0•Updated Oct 17, 2023Oct 17, 2023

    • STEMI_microbiome

      Public
      Research of microbiome in ST-Elevated Myocardial Infarction (STEMI).
      MIT License
      •0•0•0•0•Updated Sep 7, 2023Sep 7, 2023

    • Fecal_Metabolites_IBD

      Public
      Fecal Metabolomics in 255 non-IBD and 495 IBD samples
      HTML
      •1•3•0•0•Updated Jun 2, 2023Jun 2, 2023

    • GUTS_MGS_Psych

      Public
      Analysis scripts GUTS project. Metagenomics shotgun sequencing association with psychiatric patients.
      R
      •1•0•0•0•Updated Apr 26, 2023Apr 26, 2023

    • TransplantLines

      Public
      TransplantLines project
      rmicrobiome
      R
      •
      MIT License
      •2•1•0•0•Updated Feb 19, 2023Feb 19, 2023

    • SNV_Calling-Association

      Public
      Scripts for calling microbiome SNV and downstream analysis
      R
      •0•0•0•0•Updated Aug 29, 2022Aug 29, 2022

    • DMP_MentalHeath

      Public
      Dutch Microbiome Project, gut-brain axis
      1•1•0•0•Updated Jul 14, 2022Jul 14, 2022

    • SV_BA

      Public
      Metagenome-wide SV-based association study on bile acids
      R
      •0•1•0•0•Updated Oct 21, 2021Oct 21, 2021

    • DMP_GWAS

      Public
      Dutch Microbiome Project GWAS
      Shell
      •1•0•0•0•Updated Sep 27, 2021Sep 27, 2021

    • DMP

      Public
      Codes and sample data supporting the Dutch Microbiome Project. The preprint is currently available at https://www.biorxiv.org/content/10.1101/2020.11.27.401125v1 and full data can be requested from EGA (https://ega-archive.org/studies/EGAS00001005027) and Lifelines biobank (https://www.lifelines.nl/researcher)
      rmicrobiome
      HTML
      •18•32•0•0•Updated Jun 24, 2021Jun 24, 2021