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annotateme

AnnotateMe is an annotation framework for single nucleotide polymorphisms. Can be used to annotate genetic variants to likely affected genes and to perform gene-set overlap analysis of the associated genes.

centenarians_ad

Script to perform association analysis and downstream analysis of SNP associated with Alzheimer's disease (AD) in a cohort of cognitively healthy centenarians.

centenassoc

Pipeline to perform replication of genetic variants associated with longevity in previous studies by looking at the reported variants, their haplotype, the genes these variants are associated with, and polygenic risk scores.

disentangle_ad_age

Script for the analysis of the imbalance effect direction between Alzheimer's disease and cognitively healthy aging

jordan

R script to calculate Polygenic Risk Score from genotype data, and eventually plot them.

ldsc

LD Score Regression (LDSC)

locuznicco

The tools is supposed to create locusplots of the association of genetic variants in a given dataset

pacbio_pipeline

pathway-prs

Pipeline to perform annotation of variants to a pre-selected set of pathways and then calculate and associate pathway-specific Polygenic Risk Scores (PRS) and typical PRS.

scramble

In order to address the concerns regarding the privacy of genetic data and the need to perform genotype imputation relying on a server that is located in the United States, we have developed a pipeline to randomly shuffle chromosomes across a set of individuals which makes it virtually impossible to reconstruct each individual’s genotype at full genomic scale. The only way to reconstruct each individual’s genotype at full genomic scale is through a key file, which is safely stored in our servers and it is not shared.

snpxplorer

SNPbrowser is project written in python to display results from Genome-Wide Association Studies (GWAS) with a wide range of possibilities, including overlap of multiple studies.