Open resources

Open resources from the Sleegers lab

Browse datasets, code and pipelines linked to our publications and consortia work (EADB, EMIF, CMN). Reuse encouraged—please cite the associated paper and DOI.

Questions or requests? Open an issue on GitHub or get in touch.

Sleegers lab GitHub

Lab-wide repositories for analyses, utilities and reproducible workflows.
https://github.com/SleegersLab-VIBCMN

EADB QTL/TWAS datasets

Public GitHub repository outlining the Zenodo repositories hosting significant eQTL/sQTL catalogues and expression/splicing TWAS reference panels and Nanopore cDNA sequencing experiment for TSPAN14 splicing analysis prepared Bellenguez, Küçükali, et al. Nature Genetics (2022) publication (https://www.nature.com/articles/s41588-022-01024-z).

https://github.com/SleegersLab-VIBCMN/EADB_GWAS_NatureGenetics_QTL_TWAS
- the Zenodo repository for the significant eQTLs and expression TWAS reference panels: https://doi.org/10.5281/zenodo.5745927
- the Zenodo repository for the significant sQTLs and splicing TWAS reference panels): https://doi.org/10.5281/zenodo.5745929
- the Nanopore cDNA sequencing experiment for TSPAN14 splicing analysis: https://www.ebi.ac.uk/ena/browser/view/PRJEB49234

EMIF AD biomarkers — rare variant analyses

Public GitHub repository for the analysis scripts and full summary statics data of the manuscript "Whole-exome rare variant analysis of Alzheimer’s disease and related biomarker traits" by Küçükali et al., Alzheimer's and Dementia (2022), https://doi.org/10.1002/alz.12842
https://github.com/SleegersLab-VIBCMN/AD_Biomarkers_RareVariantAnalyses

EMIF AD CSF biomarker profiles — multivariate GWAS scripts

Public GitHub repository for analysis scripts for "Multivariate GWAS of Alzheimer’s disease CSF biomarker profiles implies GRIN2D in synaptic functioning", Neumann et al., Genome Medicine (2023), https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-023-01233-z

https://github.com/aneumann-science/common_variants_csf_biomarkers

EMIF AD CSF biomarker profiles — multivariate GWAS data

Zenodo repository hosting the summary statistics for a genome-wide association study (GWAS) of Alzheimer's disease CSF biomarkers principal components (PCs), as described in Neumann et al., Genome Medicine (2023), https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-023-01233-z

https://zenodo.org/records/8334941

EMIF AD CSF biomarker profiles — rare variant analyses scripts

Public GitHub repository for analysis scripts for "Rare variants in IFFO1, DTNB, NLRC3 and SLC22A10 associate with Alzheimer’s disease CSF profile of neuronal injury and inflammation", Neumann et al., Molecular Psychiatry (2022), https://www.nature.com/articles/s41380-022-01437-6

https://github.com/aneumann-science/rare_variants_csf_biomarkers

sCJD multi-omic QTL/TWAS/PWAS results

Zenodo repository hosting the full e/pQTL-GWAS coloc and TWAS/PWAS results from our study "Multiomic analyses direct hypotheses for Creutzfeldt-Jakob disease risk genes" by Küçükali & Hill et al. Brain (2025) https://academic.oup.com/brain/advance-article/doi/10.1093/brain/awaf032/7981667

https://zenodo.org/records/12507355

scywalker

Public GitHub repository for scywalker, a pipeline we co-developed for accurate, scalable, and comprehensive analysis of long-read single nucleus RNA sequencing datasets as described in De Rijk et al., Bioinformatics (2024) https://academic.oup.com/bioinformatics/article/40/9/btae549/7754485

https://github.com/derijkp/scywalker

inquiSTR

Public GitHub repository for inquiSTR, a toolset developed by Dr. Wouter De Coster. We contributed by developing an R script (STR_regression.R) that performs efficient genome-wide or targeted association testing on known tandem repeats genotyped by inquiSTR, followed by detailed result annotation

https://github.com/wdecoster/inquiSTR