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adap-in-mzmine2

anorexiagutmicrobiome

biobakery

bioBakery tools for meta'omic profiling

biobakery_workflows

bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.

broade_hailworkshop2020

Workshop materials used during the BroadE Hail Workshop in 2020 held by the BroadE monthly learning platform.

chipimputation

Genotype Imputation Pipeline for H3Africa

ckg

Clinical Knowledge Graph (CKG) is a platform with twofold objective: 1) build a graph database with experimental data and data imported from diverse biomedical databases 2) automate knowledge discovery making use of all the information contained in the graph

codebase

Code depository for papers

complexheatmap

Make Complex Heatmaps

cvrisk

R package to calculate cardiovascular risk scores

dataprep

start with raw plink, end with standardized QCed plink

demo_codes

diab_gsmm_t1d

Scripts for data analysis and GSMM – Diabimmune T1D study

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)

funkyheatmap

Visualising data frames as funky heatmaps 📊

genetics-colocalisation

Colocalisation pipeline for Open Targets Genetics

gengen

A set of software tools to facilitate GWAS analysis

groningen-microbiome

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

gsmm_t1d

Genome-scale modeling and meta-'omics' data analysis in T1D

gtc2vcf

Tools to convert Illumina IDAT/BPM/EGT/GTC and Affymetrix CEL/CHP files to VCF

gwa_tutorial

A comprehensive tutorial about GWAS and PRS

h3agwas

GWAS Pipeline for H3Africa

h3agwas-examples

humann

HUMAnN 3.0 is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).

imputationserver

Michigan Imputation Server: A new web-based service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity

introduction-to-seurat-package

Single Cell RNA sequencing Analysis. QC, transform, scaling, clustering and Biomarker identification

irfinder

Scheduled for testing

kneaddata

Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.

krona

Interactively explore metagenomes and more from a web browser.

louper

Convert Seurat objects to 10x Genomics Loupe files.