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    112 repositories

    • savant

      Public
      Sparse Allele Vector AssociatioN Tool
      C++
      •
      Mozilla Public License 2.0
      •0•0•0•0•Updated Dec 23, 2024Dec 23, 2024

    • bravo_data_prep

      Public
      Work flows and tools to create data that backs the BRAVO API.
      C++
      •
      MIT License
      •2•0•6•0•Updated Dec 9, 2024Dec 9, 2024

    • bravo_vue

      Public
      BRAVO's Vue JS based UI.
      Vue
      •0•0•14•13•Updated Dec 5, 2024Dec 5, 2024

    • topmed_variant_calling

      Public
      C++
      •
      Apache License 2.0
      •3•23•3•0•Updated Nov 27, 2024Nov 27, 2024

    • bravo_api

      Public
      Server side data processing and retrieval endpoints for BRAVO
      Python
      •
      MIT License
      •2•1•16•0•Updated Nov 19, 2024Nov 19, 2024

    • 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 productivity
      Java
      •
      GNU Affero General Public License v3.0
      •43•6•0•0•Updated Nov 5, 2024Nov 5, 2024

    • nullmetal

      Public
      C++
      •0•0•0•0•Updated Sep 6, 2024Sep 6, 2024

    • encore

      Public
      Encore Analysis Server
      Python
      •
      GNU Affero General Public License v3.0
      •6•13•0•5•Updated Aug 23, 2024Aug 23, 2024

    • terraform-aws-imputation-server

      Public
      A set of Terraform Modules for deploying an imputation server on AWS
      awsbioinformaticsterraformterraform-modules
      HCL
      •
      Apache License 2.0
      •2•1•0•0•Updated Aug 19, 2024Aug 19, 2024

    • raremetal

      Public
      A flexible tool for meta-analysis
      gwas
      C++
      •8•9•29•1•Updated Jul 31, 2024Jul 31, 2024

    • nextflow-sc_dge

      Public
      R
      •
      MIT License
      •4•0•0•0•Updated Jul 31, 2024Jul 31, 2024

    • pheweb

      Public
      A tool to build a website to browse hundreds or thousands of GWAS.
      Python
      •
      MIT License
      •67•164•36•1•Updated Jul 31, 2024Jul 31, 2024

    • EPID731_2024

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jul 30, 2024Jul 30, 2024

    • cloudgene

      Public
      A framework to build Software As A Service (SaaS) platforms for data analysis pipelines.
      Java
      •
      GNU Affero General Public License v3.0
      •19•0•0•0•Updated Jul 25, 2024Jul 25, 2024

    • METAL

      Public
      Meta-analysis of genomewide association scans
      C++
      •
      Other
      •13•49•23•1•Updated Jul 18, 2024Jul 18, 2024

    • vuptool

      Public
      Tool for detecting and handling genomic variant under methylation probes
      C++
      •
      Mozilla Public License 2.0
      •0•0•0•0•Updated Jul 7, 2024Jul 7, 2024

    • demuxlet

      Public
      Genetic multiplexing of barcoded single cell RNA-seq
      C++
      •
      Apache License 2.0
      •26•122•72•3•Updated Jul 1, 2024Jul 1, 2024

    • savvy

      Public
      Interface to various variant calling formats.
      C++
      •
      Mozilla Public License 2.0
      •6•26•9•1•Updated Jun 15, 2024Jun 15, 2024

    • hds-util

      Public
      C++
      •
      Mozilla Public License 2.0
      •0•2•4•0•Updated Apr 22, 2024Apr 22, 2024

    • encore-client-r

      Public
      An R package to interact with the Encore analysis server
      R
      •0•2•1•0•Updated Feb 28, 2024Feb 28, 2024

    • telomere-length-pipeline

      Public
      A cloud-based pipeline to estimate telomere lengths from WGS data using Telseq
      WDL
      •1•0•0•0•Updated Feb 18, 2024Feb 18, 2024

    • bravo-infrastructure

      Public
      Provisioning and deployment of example BRAVO vignette.
      HCL
      •0•0•1•0•Updated Jan 25, 2024Jan 25, 2024

    • topmed-methylation-qtl

      Public
      PIpeline for TOPMed methylation QTL analysis.
      R
      •
      MIT License
      •0•0•0•0•Updated Jan 11, 2024Jan 11, 2024

    • Minimac4

      Public
      C++
      •
      GNU General Public License v3.0
      •21•56•45•3•Updated Dec 3, 2023Dec 3, 2023

    • rand-recom

      Public
      Tool for randomly applying artificial recombination
      C++
      •
      Mozilla Public License 2.0
      •0•0•0•0•Updated Nov 16, 2023Nov 16, 2023

    • di2hap

      Public
      A tool for converting diploid geontypes to haploid.
      CMake
      •
      Mozilla Public License 2.0
      •0•0•0•0•Updated Nov 8, 2023Nov 8, 2023

    • ansible-bravo-deploy

      Public
      Anisble deployment roles and playbook for BRAVO API and UI
      Jinja
      •0•0•1•0•Updated Oct 24, 2023Oct 24, 2023

    • LDServer

      Public
      Fast API server for calculating linkage disequilibrium
      genetics
      C++
      •
      GNU General Public License v3.0
      •2•17•3•4•Updated Aug 6, 2023Aug 6, 2023

    • ruth

      Public
      Robust Unified Hardy-Weinberg Equilibrium Test
      C++
      •
      Apache License 2.0
      •2•6•8•0•Updated May 22, 2023May 22, 2023

    • libStatGen

      Public
      Useful set of classes for creating statistical genetic programs.
      C++
      •29•52•9•3•Updated May 15, 2023May 15, 2023