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cs_baby_biome

dmp

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)

dmp_gwas

Dutch Microbiome Project GWAS

dmp_mentalheath

Dutch Microbiome Project, gut-brain axis

fecal_metabolites_ibd

Fecal Metabolomics in 255 non-IBD and 495 IBD samples

groningen-microbiome

Microbiome Projects from the Department of Genetics and Department of Gastroenterology and Hepatology , University Medical Centre Groningen

guts_mgs_psych

Analysis scripts GUTS project. Metagenomics shotgun sequencing association with psychiatric patients.

lifelines_next

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 Northern Netherlands. In Lifelines NEXT we include 1500 pregnant women intensively follow them, their partners and their children until at least 1 year after birth. This repository describes the codes for the microbiome associated projects within Lifelines NEXT including fecal (microbiome and virome), breastmilk microbiome, vaginal mcirobiome and oral microbiome. Here we also integrate mutpliple multi-omic layers including metabolomics, proteomics and extensive phenotypic data

lifelines_next_milk_microbiota

Research of mother milk and infant microbiome

llnext_pilot

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.

microberx

MicrobeRX

milkmethods2023

phip-seq_lld-ibd

Scripts for data analysis of Phip-Seq (microbial and allergen libraries) in LLD and 1000IBD studies

snv_calling-association

Scripts for calling microbiome SNV and downstream analysis

stemi_microbiome

Research of microbiome in ST-Elevated Myocardial Infarction (STEMI).

sv_ba

Metagenome-wide SV-based association study on bile acids

sv_gwas

This repository contains the code used for SV-GWAS project

sv_ibd

transplantlines

TransplantLines project