This repository contains code from:
Mikhail D. Magnitov, Robin H. van der Weide†, Aster F. Witvliet†, Miguel Hernández Quiles, Moreno Martinović, Hans Teunissen, Luca Braccioli, Michiel Vermeulen, Elzo de Wit. Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning (2025)
- variants: selection of samples, variants data processing
- 10X: 10X linked-reads data processing
- HiC: Hi-C data processing
- simulations: TELL-seq and stLFR data processing, data subsampling for phasing quality estimation
- personal_genomes: whole-chromosome haplotyping, phased heterozygous variants, and personal genomes construction
- ATACseq: ATAC-seq data processing, quantification, and analysis
- TTseq: TT-seq data processing, quantification, and analysis
- ChIPseq: ChIP-seq data processing
- links: putative regulatory links analysis
- ChromBPNet: trained models, predicted contribution scores, and disrupted motifs analysis
- validation: validation data for the rs545467951 variant
Sequencing data have been deposited at GEO database (GSE308298). Proteomics data have been deposited at PRIDE database (PXD069116). Supporting data necessary to reproduce the results presented in this manuscript have been deposited at Zenodo (https://doi.org/10.5281/zenodo.17285189).