-- TODO add introduction to vntrs
This is a shiny R app to browse minisatellites polymorphism and characteristics in the human genome. The data used comes from:
Rasekh, Marzieh Eslami, et al. "Genome-wide characterization of human minisatellite VNTRs: population-specific alleles and gene expression differences." bioRxiv (2020).
and the raw data is publically available on Zenodo DOI 10.5281/zenodo.4065850
The available functions are:
- Search: You can search minisatellite loci by position in the genome (GRCh38), overlapping gene, or by TRDB id. The loci can be filtered down by characteristics, i.e. polymorphic in various population, having population biased alleles, being in eqtl with genes, or not following the Hardy Weingerg equilibrium.
- Genome browser: Visualize the minisatellite and the annotation in the UCSC genome browser. This can be useful to find overlapping genes, regulatory regions, histon markers, common SNPs or other variants.
- Population-biased VNTR alleles: Illustrate alleles by population (from the 1000 Genomes Project) and apply fisher-exact test to find population biased alleles.
- eQTL VNTRs: Display the gene expression of 465 samples from E-GEUV-1 for each VNTR genotype and the association.
- Haplotypes: Under construction.
There is an online bioinformatics tools available:
- Wrap-around alignment to find copy number of a given pattern in one or more sequences.
Authors: Marzie Eslami Rasekh (PhD candidate, Boston University), Michael P. Griffin (A boring place who no one knows what they do.)
License: Do what ever you want.
Citation: TBD