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    428 repositories

    • NEDSS-Modernization

      Public
      Java
      •4•20•0•5•Updated Feb 17, 2025Feb 17, 2025

    • ixa-epi-isolation

      Public
      Rust
      •
      Apache License 2.0
      •2•1•9•4•Updated Feb 17, 2025Feb 17, 2025

    • Opioid_SUD_MHI_MedCodes

      Public
      Code to flag ICD-10-CM codes related to opioid involvement, substance use disorder, and mental health issues in structured hospital data
      Python
      •6•6•0•0•Updated Feb 17, 2025Feb 17, 2025

    • phoenix

      Public
      🔥🐦🔥PHoeNIx: a platform agnostic pipeline for healthcare-associated and antimicrobial resistant pathogens
      Python
      •
      Apache License 2.0
      •26•67•15•1•Updated Feb 17, 2025Feb 17, 2025

    • eMKF

      Public
      SAS
      •
      Apache License 2.0
      •3•2•0•0•Updated Feb 16, 2025Feb 16, 2025

    • clean-genes

      Public
      A rust crate that automatically cleans up a gene alignment by trimming to ORF and identifying and/or removing problematic sequences.
      data-sciencebioinformaticsfastadata-normalizationdata-cleaningsequence-alignmentsequence-analysissequence-annotationncirdncird-id
      Rust
      •
      Apache License 2.0
      •2•1•5•0•Updated Feb 16, 2025Feb 16, 2025

    • prime-simplereport

      Public
      SimpleReport is a fast, free, and easy way for COVID-19 testing facilities to report results to public health departments.
      reactjsterraformgraphqlspring-boot
      Java
      •
      Creative Commons Zero v1.0 Universal
      •61•60•193•17•Updated Feb 16, 2025Feb 16, 2025

    • prime-reportstream

      Public
      ReportStream is a public intermediary tool for delivery of data between different parts of the healthcare ecosystem.
      fhirpublic-healthcivic-techhl7
      Kotlin
      •
      Creative Commons Zero v1.0 Universal
      •42•75•1.3k•163•Updated Feb 16, 2025Feb 16, 2025

    • data-exchange-fhir

      Public
      Enterprise Data Exchange (DEX) is a new cloud-native centralized data ingestion, validation, and observation service scoped for common data types (HL7, FHIR, CDA, XML, CSV) sent to the CDC. It helps public health stakeholders who send data to the CDC while reducing the maintenance efforts, complexity, and duplication of ingestion points to CDC.
      C#
      •
      Apache License 2.0
      •5•11•157•1•Updated Feb 16, 2025Feb 16, 2025

    • ixa

      Public
      Rust
      •
      Apache License 2.0
      •2•14•31•4•Updated Feb 16, 2025Feb 16, 2025

    • tostadas

      Public
      🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission
      pythondockermetadatabioinformaticsrna-seqpipelinenextflowgeneticsazuresequencing
      Python
      •
      Apache License 2.0
      •12•27•17•1•Updated Feb 16, 2025Feb 16, 2025

    • data-exchange-upload

      Public
      The Public Health Data Operations (PHDO) Upload service provides secure ingestion, delivery, and observability of public health files from data senders to CDC program target locations via Application Programming Interfaces (APIs).
      Go
      •
      Apache License 2.0
      •6•9•42•18•Updated Feb 15, 2025Feb 15, 2025

    • NEDSS-DataIngestion

      Public
      Data Ingestion for Modernization of NEDSS Project by Enquizit
      Java
      •
      Apache License 2.0
      •4•6•0•9•Updated Feb 14, 2025Feb 14, 2025

    • terraform-aws-dibbs-ecr-viewer

      Public
      HCL
      •
      Apache License 2.0
      •3•0•1•1•Updated Feb 14, 2025Feb 14, 2025

    • dibbs-query-connector

      Public
      A FHIR client allowing public health agencies to query health care organizations directly or via a TEFCA QHIN
      TypeScript
      •
      Creative Commons Zero v1.0 Universal
      •4•5•42•2•Updated Feb 14, 2025Feb 14, 2025

    • RecordLinker

      Public
      The RecordLinker is a service that links records from two datasets based on a set of common attributes. The service is designed to be used in a variety of public health contexts, such as linking patient records from different sources or linking records from different public health surveillance systems.
      pythonsqlalchemyfastapi
      Python
      •
      Apache License 2.0
      •2•3•21•2•Updated Feb 14, 2025Feb 14, 2025

    • nbbp

      Public
      Negative binomial branching process final size distributions & parameter inference
      R
      •
      Apache License 2.0
      •2•0•8•3•Updated Feb 14, 2025Feb 14, 2025

    • cfa-viral-lineage-model

      Public
      Python
      •
      Apache License 2.0
      •2•11•17•1•Updated Feb 14, 2025Feb 14, 2025

    • DynODE

      Public
      CDC/CFA/Predict/Scenarios ODE Modeling Framework
      Python
      •
      Apache License 2.0
      •2•7•44•1•Updated Feb 14, 2025Feb 14, 2025

    • dibbs-ecr-viewer

      Public
      HTML
      •
      Creative Commons Zero v1.0 Universal
      •1•2•245•5•Updated Feb 14, 2025Feb 14, 2025

    • cdc-open-viz

      Public
      CDC OpenViz is a library of React packages for data visualization.
      reactvisualizationdatavisualization-library
      TypeScript
      •
      Apache License 2.0
      •25•39•0•2•Updated Feb 14, 2025Feb 14, 2025

    • Rnssp-shiny-apps

      Public
      Rnssp Shiny Apps are custom-built applications with seamless integration to the Rnssp R package.
      shinyshiny-appscdcessencensspessence-apinssp-cop
      R
      •
      Apache License 2.0
      •6•9•4•0•Updated Feb 14, 2025Feb 14, 2025

    • cfa-immunization-uptake-projection

      Public
      Python
      •
      Apache License 2.0
      •3•1•12•2•Updated Feb 14, 2025Feb 14, 2025

    • dibbs-vm

      Public
      HCL
      •
      Creative Commons Zero v1.0 Universal
      •4•0•30•1•Updated Feb 14, 2025Feb 14, 2025

    • dibbs-aws

      Public template
      HCL
      •
      Creative Commons Zero v1.0 Universal
      •2•3•0•1•Updated Feb 14, 2025Feb 14, 2025

    • forecasttools-py

      Public
      A Python package for common pre- and post-processing operations done by CFA Predict for short term forecasting, nowcasting, and scenario modeling.
      infrastructureautomationabstractionforecastinginfectious-disease-modeling
      Python
      •
      Apache License 2.0
      •2•6•15•3•Updated Feb 14, 2025Feb 14, 2025

    • seqsender

      Public
      Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
      bioinformatics-pipelinegenbankncbi-submissionncbi-genbankcdcsrancbi-srancbi-biosamplesgisaidgisaid-uploader
      Python
      •
      Apache License 2.0
      •14•34•5•0•Updated Feb 14, 2025Feb 14, 2025

    • NEDSS-Helm

      Public
      This repository is created for NEDSS Helm charts.
      Smarty
      •
      Apache License 2.0
      •4•2•0•9•Updated Feb 14, 2025Feb 14, 2025

    • aquascope

      Public
      Nextflow
      •
      MIT License
      •14•20•3•0•Updated Feb 14, 2025Feb 14, 2025

    • pyrenew-hew

      Public
      Models and infrastructure for forecasting COVID-19 and Flu hospitalizations using wastewater data with PyRenew
      Python
      •
      Apache License 2.0
      •3•8•62•4•Updated Feb 14, 2025Feb 14, 2025