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@statgen Center for Statistical Genetics

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    120 repositories

    • cloudgene3

      Public
      A framework to build Software As A Service (SaaS) platforms for Nextflow pipelines.
      Java
      •
      MIT License
      •9•0•0•0•Updated Sep 3, 2026Sep 3, 2026

    • bravo_api

      Public
      Server side data processing and retrieval endpoints for BRAVO
      Python
      •
      MIT License
      •2•1•16•0•Updated Sep 1, 2026Sep 1, 2026

    • encore

      Public
      Encore Analysis Server
      Python
      •
      GNU Affero General Public License v3.0
      •6•13•0•4•Updated Aug 26, 2026Aug 26, 2026

    • RNA-seq-tracking

      Public
      Tracks TOPMed OMICS qc progress
      PHP
      •0•1•0•0•Updated Aug 25, 2026Aug 25, 2026

    • imputationserver2

      Public
      Imputation Server 2 workflow to facilitate genotype imputation at scale.
      Nextflow
      •
      MIT License
      •15•0•0•0•Updated Aug 18, 2026Aug 18, 2026

    • bravo_vue

      Public
      BRAVO's Vue JS based UI.
      Vue
      •0•0•13•19•Updated Jul 16, 2026Jul 16, 2026

    • tis-v2-docs

      Public
      User-facing documentation for the TOPMed Imputation Server v2 (Nextflow edition)
      0•0•0•0•Updated May 19, 2026May 19, 2026

    • tis-v2-cli

      Public
      Provides utilities to access the TOPMed Imputation Server programmatically.
      Python
      •0•1•1•0•Updated Apr 27, 2026Apr 27, 2026

    • pheweb

      Public
      A tool to build a website to browse hundreds or thousands of GWAS.
      Python
      •
      MIT License
      •75•198•38•2•Updated Apr 22, 2026Apr 22, 2026

    • savvy

      Public
      Interface to various variant calling formats.
      C++
      •
      Mozilla Public License 2.0
      •7•31•9•1•Updated Apr 10, 2026Apr 10, 2026

    • fipip

      Public
      Python
      •
      Apache License 2.0
      •0•1•0•0•Updated Mar 25, 2026Mar 25, 2026

    • imputationserver-utils

      Public
      Java
      •
      MIT License
      •4•0•0•0•Updated Feb 27, 2026Feb 27, 2026

    • colocus-ui-vue3

      Public
      JavaScript
      •0•0•0•0•Updated Feb 2, 2026Feb 2, 2026

    • ansible-bravo-deploy

      Public
      Anisble deployment roles and playbook for BRAVO API and UI
      Jinja
      •1•0•1•0•Updated Jan 16, 2026Jan 16, 2026

    • bravo_data_prep

      Public
      Work flows and tools to create data that backs the BRAVO API.
      C++
      •
      MIT License
      •2•0•8•0•Updated Jan 5, 2026Jan 5, 2026

    • colocus

      Public
      A browser for display of fine-mapped genetic signals and their colocalizations
      geneticsstatistical-geneticscolocalization
      geneticsstatistical-geneticscolocalizationfine-mapping
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 11, 2025Dec 11, 2025

    • fipip_manuscript

      Public
      Manuscript source files to reproduce fiPIP manuscript display items
      Jupyter Notebook
      •0•0•0•0•Updated Nov 24, 2025Nov 24, 2025

    • imputationserver

      Public
      TOPMED Imputation Server: A new web-based service for imputation that facilitates access to new reference panels and greatly improves user experience and produc…
      Java
      •
      GNU Affero General Public License v3.0
      •48•6•0•0•Updated Oct 20, 2025Oct 20, 2025

    • topmed-methylation-qtl

      Public
      PIpeline for TOPMed methylation QTL analysis.
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 11, 2025Oct 11, 2025

    • savant

      Public
      Sparse Allele Vector AssociatioN Tool
      C++
      •
      Mozilla Public License 2.0
      •0•0•0•0•Updated Oct 11, 2025Oct 11, 2025

    • bravo-infrastructure

      Public
      Provisioning and deployment of example BRAVO vignette.
      HCL
      •0•0•1•0•Updated Aug 26, 2025Aug 26, 2025

    • locuszoom-api

      Public
      Flask server code for LocusZoom APIs
      Python
      •
      MIT License
      •3•1•0•0•Updated Jul 7, 2025Jul 7, 2025

    • Minimac4

      Public
      C++
      •
      GNU General Public License v3.0
      •26•85•52•2•Updated Jun 4, 2025Jun 4, 2025

    • locuszoom

      Public
      A Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources.
      gwaslocuszoomgwas-tools
      gwaslocuszoomgwas-toolsgwas-summary-statisticslocuszoom-plot
      JavaScript
      •
      MIT License
      •33•170•15•4•Updated May 9, 2025May 9, 2025

    • localzoom

      Public
      Make interactive LocusZoom plots from a local GWAS file
      gwasgwas-cataloglocuszoom
      gwasgwas-cataloglocuszoomgwas-pipelinegwas-toolsgwas-summary-statisticslocuszoom-plot
      Vue
      •
      MIT License
      •5•10•0•9•Updated May 9, 2025May 9, 2025

    • locuszoom-hosted

      Public
      A web service to upload and share GWAS results with LocusZoom.js
      gwaslocuszoomgwas-pipeline
      gwaslocuszoomgwas-pipelinegwas-toolsgwas-summary-statisticslocuszoom-plot
      Python
      •
      MIT License
      •0•2•13•11•Updated May 8, 2025May 8, 2025

    • zorp

      Public
      A simple GWAS parser + CLI
      pythongwasconversion
      pythongwasconversionparserslocuszoomgwas-pipelinegwas-toolsgwas-summary-statistics
      Python
      •
      MIT License
      •0•1•2•0•Updated May 7, 2025May 7, 2025

    • filefetcher

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated May 6, 2025May 6, 2025

    • LDServer

      Public
      Fast API server for calculating linkage disequilibrium
      genetics
      genetics
      Linker Script
      •
      GNU General Public License v3.0
      •2•20•3•4•Updated Apr 24, 2025Apr 24, 2025

    • ruth

      Public
      Robust Unified Hardy-Weinberg Equilibrium Test
      C++
      •
      Apache License 2.0
      •2•7•7•0•Updated Apr 8, 2025Apr 8, 2025
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