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@GP2code Global Parkinson's Genetics Program - Code

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    24 repositories

    • PD-GeneticCharacterization-inAFRandAAC

      Public
      This is the online repository for the manuscript titled "Large-scale genetic characterization of Parkinson’s disease in the African and African admixed populations"
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Dec 30, 2024Dec 30, 2024

    • GBA1-rs3115534-branchpoint

      Public
      This is the online repository for the manuscript titled "African ancestry neurodegeneration risk variant disrupts an intronic branchpoint in GBA1"
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Dec 30, 2024Dec 30, 2024

    • releases

      Public
      Code from various GP2 releases in perpetuity.
      WDL
      •1•1•0•0•Updated Dec 27, 2024Dec 27, 2024

    • .github

      Public
      0•0•0•0•Updated Dec 27, 2024Dec 27, 2024

    • GenoTools

      Public
      A suite of tools for processing genotype data. Includes calling genotypes from .idat to plink (ped), sample/case-control variant QC steps, ancestry estimation. UNDER DEVELOPMENT
      Python
      •
      Apache License 2.0
      •7•14•0•0•Updated Dec 17, 2024Dec 17, 2024

    • CNV-Finder

      Public
      Expedite large-scale identification of CNVs within predefined genomic regions. Online app available for those with GP2 Tier 2 Access.
      Python
      •
      Apache License 2.0
      •2•10•0•0•Updated Nov 26, 2024Nov 26, 2024

    • DNAJC13-PD-GeneBurden

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Nov 26, 2024Nov 26, 2024

    • pathogenic_pd_variants_clusters

      Public
      Simple browser for the GP2 Hackathon project looking at pathogenic Parkinson's Disease variants
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Nov 26, 2024Nov 26, 2024

    • PAR-ADPD

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Sep 25, 2024Sep 25, 2024

    • EUR_LRRK2_pL1795F

      Public
      This is the online repository for the manuscript titled "The LRRK2 p.L1795F variant causes Parkinson’s disease in the European population"
      0•0•0•0•Updated Aug 20, 2024Aug 20, 2024

    • GP2-AFR-AAC-metaGWAS

      Public
      All materials for "Genome-wide Association Identifies Novel Etiological Insights Associated with Parkinson’s Disease in African and African Admixed Populations"
      Jupyter Notebook
      •1•4•1•0•Updated Aug 15, 2024Aug 15, 2024

    • NeuroBoosterArray

      Public
      Process and code for building content lists for NeuroBoosterArray.
      1•0•0•0•Updated Jul 11, 2024Jul 11, 2024

    • GP2-WorkingGroups

      Public
      These are repositories and projects directly from GP2 members
      WDL
      •2•0•0•0•Updated May 13, 2024May 13, 2024

    • multiancestry-PRS_PRSice

      Public
      Jupyter Notebook
      •0•0•0•0•Updated May 3, 2024May 3, 2024

    • chrM.2158-analysis

      Public
      Investigating the protective role of the mitochondrial 2158 T > C variant in Parkinson’s disease
      Jupyter Notebook
      •0•0•0•0•Updated Apr 22, 2024Apr 22, 2024

    • LTFinFoxInsight

      Public
      Repository of code used for manuscript "Risk Factors for Attrition in an Online Longitudinal Study on Parkinson’s Disease"
      Jupyter Notebook
      •1•0•0•0•Updated Jan 23, 2024Jan 23, 2024

    • amp-pd-v3-pc-prs

      Public
      PC and PRS calculation for the AMP-PD release v3 WGS data
      Jupyter Notebook
      •0•1•0•0•Updated Nov 10, 2023Nov 10, 2023

    • GBA1_RBD_NIGERIA

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Oct 2, 2023Oct 2, 2023

    • GP2-Multiancestry-metaGWAS

      Public
      2•9•1•0•Updated Jun 16, 2023Jun 16, 2023

    • open_targets_api_utils

      Public
      This repository contains functions for querying open targets
      Jupyter Notebook
      •2•0•0•0•Updated Nov 18, 2020Nov 18, 2020

    • rare_variants

      Public
      This project is attempting to use missing heritability to find rare variants related to Parkinson's Disease
      Jupyter Notebook
      •1•0•0•0•Updated Nov 6, 2020Nov 6, 2020

    • deprecated_archive

      Public
      Repository for the Neuro Booster Array developed in part by Data Tecnica International, NIA, NINDS, GP2 and Illumina. We lovingly refer to it as the "NBA"!
      1•3•0•0•Updated Sep 22, 2020Sep 22, 2020

    • Allele-Set-MD5-Hash

      Public
      Python
      •1•0•0•0•Updated May 29, 2020May 29, 2020

    • genomestudio

      Public
      A few methods of using Illumina's Genome Studio for genotype calling
      Python
      •1•1•0•0•Updated Apr 28, 2020Apr 28, 2020