FOSS @ CDC

Free, Open-Source Software Built By CDC

Tools for Managing, Visualizing, Analyzing Public Health Data

A remake of CDC Portal Site

Search by Project Name:

Total Projects: 246

.github

special readme repo

0 Forks

0 Issues

2022-11-03

0 Forks

0 Issues

2021-11-30

JavaScript

AlignmentViewer

A lightweight visualization for genetic sequence alignments

2 Forks

7 Issues

2018-02-07

api-standards

API Standards for 18F

1 Forks

0 Issues

2018-04-09

Ruby

artemis

An application to assist Utah CDC's Newborn Screening Program

1 Forks

0 Issues

2017-12-25

bioseq-js

A fast, lightweight implementation of Smith-Waterman

2 Forks

2 Issues

2017-05-19

Java

blockchain-collab

CDC collaboration on blockchain prototypes.

3 Forks

0 Issues

2017-08-24

blockchainTB

Proof of project for CDC's r&d with using blockchain to support TB

5 Forks

7 Issues

2018-03-30

Python

BMGAP

The Bacterial Meningitis Genome Analysis Platform, an analysis pipeline, ExpressJS API, and ReactJS webapp for the analysis and characterization of bacterial meningitis samples

5 Forks

33 Issues

2020-06-26

HTML

Bubbles

A Simple Demonstration of Organizing Bubbles using D3v5

1 Forks

0 Issues

2019-02-11

Java

cancer-report-validator

The Cancer Report Validator (CRV) is an interactive tool for validating the content of electronic submissions of cancer-related medical information prior to a system's communication with a public health central cancer registry.

4 Forks

17 Issues

2019-12-17

JavaScript

CDC-Maps

React component for visualizing your data on a map of the United States based off work done for the CDC

2 Forks

1 Issues

2019-08-26

JavaScript

cdc-open-viz

CDC OpenViz is a library of React packages for data visualization.

5 Forks

6 Issues

2020-12-14

HTML

cdcgov.github.io

Portal site for all CDCgov projects, https://cdcgov.github.io

13 Forks

5 Issues

2016-05-13

Java

CDC_IIS_Open_Tools

The purpose of this project is to deliver tools that support production and consumption of HL7 and flat file formats used to communicate COVID-19 vaccination data between IIS and CDC to support tracking of vaccination progress for COVID-19.

8 Forks

0 Issues

2020-10-29

code-of-conduct

18F's code of conduct.

11 Forks

0 Issues

2016-02-17

1 Forks

0 Issues

2017-02-25

Shell

containers-quickstarts

PaaS & Containers CoP Application Demo Libarary

1 Forks

0 Issues

2018-10-02

Shell

couchdb

1 Forks

0 Issues

2017-09-29

0 Forks

0 Issues

2020-06-07

covid19healthbot

[Retiring Oct 7th, 2022] This project collects automated screening protocols and self-checker algorithms from organizations implementing CDC screening protocols in interactive web sites, chat bots, and other technology.

44 Forks

0 Issues

2020-03-26

0 Forks

0 Issues

2021-03-18

R

covid_case_privacy_review

Privacy review and statistical disclosure control methods for covid public case data.

5 Forks

1 Issues

2020-09-17

1 Forks

0 Issues

2022-04-18

1 Forks

1 Issues

2022-07-06

C#

cs-sdk-dotnet

SDK for working with case notification messages and message mapping guides

2 Forks

2 Issues

2021-10-19

HTML

CSV2FASTA

A little web tool to help people translate CSVs to FASTA and vice-versa.

3 Forks

1 Issues

2019-04-23

ctf-terraform-examples

Example demo of terraform functionality

1 Forks

0 Issues

2018-12-20

0 Forks

0 Issues

2017-09-01

Python

Dash_FileUploader

Dash Demonstration of the File Uploader and Dynamic Populating Dropdown Menu

1 Forks

0 Issues

2020-05-15

data-exchange

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.

0 Forks

1 Issues

2022-07-05

0 Forks

0 Issues

2022-11-10

data-exchange-fhir

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.

0 Forks

106 Issues

2022-07-05

Kotlin

data-exchange-hl7

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.

0 Forks

124 Issues

2022-07-05

Python

data-exchange-hl7-dbx

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.

2 Forks

1 Issues

2022-11-07

data-exchange-portal

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.

0 Forks

0 Issues

2022-11-30

Kotlin

data-exchange-upload

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.

1 Forks

24 Issues

2022-08-16

data-exchange-validation-csv

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.

0 Forks

0 Issues

2022-11-30

data-exchange-validation-xml

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.

0 Forks

0 Issues

2022-11-30

11 Forks

3 Issues

2021-08-09

3 Forks

2 Issues

2019-06-13

Dockerfile

docker-maven

This is the repository for the CDCgov Maven Docker image tags

2 Forks

0 Issues

2018-11-05

1 Forks

0 Issues

2017-09-29

JavaScript

environmental-health-smart-fhir

SMART on FHIR app to integrate environmental health data

1 Forks

0 Issues

2018-08-06

6 Forks

0 Issues

2020-12-15

JavaScript

ephtracking-api-assistant

Easily generate API call statements for accessing data from ephtracking.cdc.gov

2 Forks

1 Issues

2018-06-19

0 Forks

0 Issues

2021-07-21

0 Forks

0 Issues

2021-07-21

JavaScript

ephtracking-viz

Environmental Public Health Visualizations

1 Forks

0 Issues

2018-06-19

JavaScript

ephtracking-viz-assistant

Assistant that helps you to create environmental health visualizations that easily can be embedded in your website

1 Forks

0 Issues

2018-06-18

0 Forks

0 Issues

2022-07-18

R

EPHTrackR

R interface to the CDC National Public Health Tracking Network API

3 Forks

13 Issues

2021-04-21

C#

erhms-info-manager

Data collection and analysis tools designed to help emergency response organizations implement the Emergency Responder Health Monitoring and Surveillance (ERHMS) framework

1 Forks

0 Issues

2020-05-12

JavaScript

ex-ui-datalake-dashboard

Example UI for a Datalake Dashboard

3 Forks

0 Issues

2018-11-13

JavaScript

ex-ui-hl7-combiner

Example UI for an HL7 Combiner Tool

3 Forks

0 Issues

2018-10-31

2 Forks

1 Issues

2021-03-24

F2017CDCLiaison

Deliverables and Status reports from CS 6440 Introduction to Health Informatics

3 Forks

0 Issues

2017-10-30

fdns

This is a central repository with high level information on Foundation Services, tutorials, example code, etc.

6 Forks

0 Issues

2018-04-03

Java

fdns-java-sdk

This is the repository with the Java SDK for Foundation Services.

7 Forks

0 Issues

2018-04-03

JavaScript

fdns-js-sdk

This is the repository with the JavaScript SDK for Foundation Services.

4 Forks

0 Issues

2018-04-03

Java

fdns-kafka-library

This is the repository with the Java Library for Foundation Services Kafka workers.

3 Forks

0 Issues

2018-09-06

FreeMarker

fdns-ms-cda-utils

This is the repository with the CDA utilities service to parse, validate and generate sample CDA data.

3 Forks

0 Issues

2018-04-03

Java

fdns-ms-combiner

This is the repository with the Combiner service to combine JSON files into a single CSV or XLSX file.

8 Forks

0 Issues

2018-04-03

fdns-ms-crypto

This is the repository for the cryptography microservice.

1 Forks

0 Issues

2018-08-09

HTML

fdns-ms-gateway

This is the repository with the API gateway to connect the other microservices together.

4 Forks

0 Issues

2018-04-03

Java

fdns-ms-hl7-utils

This is the repository with the HL7 utilities service to parse, validate and generate sample HL7 data.

9 Forks

3 Issues

2018-04-03

Java

fdns-ms-indexing

This is the repository with the Indexing layer for the Data Lake. This is the navigation layer.

6 Forks

0 Issues

2018-04-03

Java

fdns-ms-msft-utils

This is the repository with the Microsoft Utilities microservice for parsing Microsoft formatted documents.

6 Forks

0 Issues

2018-08-09

Java

fdns-ms-object

This is the repository with the Object layer for the Data Lake. This is the mutable layer.

7 Forks

0 Issues

2018-04-03

Java

fdns-ms-reporting

This is the repository for the reporting microservice.

5 Forks

0 Issues

2018-08-09

Java

fdns-ms-reporting-kafka

This is the repository that contains the Kafka workers to handle the generation of reports.

4 Forks

1 Issues

2018-08-09

Java

fdns-ms-rules

This is the repository with the Business Rules Engine for ingesting and validating JSON files.

7 Forks

0 Issues

2018-04-03

Java

fdns-ms-storage

This is the repository with the Storage layer for the Data Lake. This is the immutable layer.

8 Forks

0 Issues

2018-04-03

JavaScript

fdns-ms-stubbing

A stubbing service for testing against the various endpoints of the FDNS Microservices without running the full microservices in the background.

3 Forks

0 Issues

2018-12-07

Java

fdns-rules-engine

This the repository with the Java Library for the Business Rules Engine.

4 Forks

0 Issues

2018-04-03

HTML

fdns-ui

Testing GitHub Pages for FDNS-UI

1 Forks

0 Issues

2019-09-02

JavaScript

fdns-ui-react

A collection of reusable React components for quickly building modern and accessible web applications.

7 Forks

19 Issues

2018-04-03

JavaScript

fdns-ui-react-docs

This project includes documentation and examples for the FDNS React UI Library.

2 Forks

0 Issues

2018-11-13

JavaScript

fileto

A little library to work with Javascript File objects

1 Forks

0 Issues

2018-12-14

Flu

Repository for CDC's Flu Division

2 Forks

0 Issues

2016-08-24

Shell

fluentd

1 Forks

0 Issues

2017-09-29

1 Forks

0 Issues

2021-11-18

XSLT

GaTech-Fall2017-Davis-dohMPI-SPYNdoctors

GaTech-Fall2017-Davis-dohMPI-SPYNdoctors

1 Forks

0 Issues

2017-11-28

JavaScript

GaTech-Fall2017-Duncan-BirthCerts-iHealth

GaTech-Fall2017-Duncan-BirthCerts-iHealth

1 Forks

0 Issues

2017-11-28

JavaScript

GaTech-Fall2017-Goodman-HealthWeight-TeamScienceFreaks

GaTech-Fall2017-Goodman-HealthWeight-TeamScienceFreaks

1 Forks

0 Issues

2017-11-28

C#

GaTech-Fall2017-Krupa-Concussion-FHIRStarters

GaTech-Fall2017-Krupa-Concussion-FHIRStarters

1 Forks

0 Issues

2017-11-27

Ruby

GaTech-Fall2017-Newborn-FHIRFighters

GaTech-Fall2017-Newborn-FHIRFighters

1 Forks

0 Issues

2017-11-28

JavaScript

GaTech-Fall2017-Srinivasan-ImproveAdherence-DEVSonFHIR

GaTech-Fall2017-Srinivasan-ImproveAdherence-DEVSonFHIR

1 Forks

0 Issues

2017-11-28

JavaScript

GaTech-Fall2017-Srinivasan-SocialDeterminant-GT-MKSM

GaTech-Fall2017-Srinivasan-SocialDeterminant - GT-MKSM

1 Forks

0 Issues

2017-11-28

Java

GaTech-Fall2017-Srinivasan-Stroke-Team1

GaTech-Fall2017-Srinivasan-Stroke-Team1

1 Forks

0 Issues

2017-11-28

JavaScript

GaTech-Fall2017-Wilmore-Breastfeeding-WeDidntStartTheFHIR

GaTech-Fall2017-Wilmore-Breastfeeding-WeDidntStartTheFHIR

0 Forks

0 Issues

2017-11-28

Python

geneflow

GeneFlow: A Workflow Engine for Bioinformatics and Public Health Analytics

6 Forks

0 Issues

2019-03-19

geneflow-workflows

GeneFlow Public Reference Workflows

1 Forks

0 Issues

2020-04-07

Python

geneflow2

GeneFlow: A Workflow Engine for Bioinformatics and Public Health Analytics

2 Forks

0 Issues

2020-04-15

gift

Gold Idea First Templates covering data, analytics and visualization.

2 Forks

0 Issues

2021-12-28

hackathon2018

This is the repository for the projects from the 2018 Open CDC Hackathon

10 Forks

8 Issues

2018-10-04

HTML

HantaNet

Standalone Hantavirus visualization engine, powered by MicrobeTrace

4 Forks

2 Issues

2021-02-22

Python

hie-automation-tests

HIE Automation testing framework - OpenMRS, OpenHIM, OpenSHR, HAPI-FHIR, OpenEMPI

5 Forks

2 Issues

2020-12-10

1 Forks

0 Issues

2019-08-07

Python

idmp-sas-to-csv

SAS to CSV microservice

1 Forks

0 Issues

2018-03-05

R

IMslide_1

Generation of figure by routine reporting for the case surveillance section used for IM slide 1 during summer of 2020 for COVID19 response

2 Forks

0 Issues

2020-09-25

R

ITF-Dashboard

A code-only repo of the ITF Dashboard backend

0 Forks

0 Issues

2022-05-11

R

ITF_Power_BI

Contains functions for pulling publicly-available global COVID-19 case and testing data for analysis and populating a Power BI dashboard.

16 Forks

2 Issues

2020-07-15

Shell

jenkins

1 Forks

0 Issues

2019-08-19

Dockerfile

jenkins-agent-sonarqube

Jenkins worker container image for performing a sonarqube CLI scan

1 Forks

0 Issues

2018-11-01

C

jq

Command-line JSON processor

1 Forks

0 Issues

2018-12-04

1 Forks

0 Issues

2017-09-29

2 Forks

0 Issues

2017-09-29

Shell

kibana

1 Forks

0 Issues

2017-09-29

KPIP

Kmer Pathogen Identification Platform

1 Forks

0 Issues

2020-05-29

Shell

legionella_pneumophila_genomics

This repository contains bioinformatics scripts and a Docker container to perform the in silico prediction of Legionella pneumophila serogroup from short read sequences using a supervised machine learning approach.

5 Forks

2 Issues

2019-10-07

2 Forks

1 Issues

2021-01-25

1 Forks

0 Issues

2017-09-29

Python

LpSubP

LpSubP is a rapid subtyping tool for Legionella pneumophila with core gene set

4 Forks

2 Issues

2019-09-27

Malaria_HFS

This repository provides tool templates for malaria focused health facility surveys.

0 Forks

0 Issues

2022-04-12

Jupyter Notebook

MaRS

See Readme

8 Forks

0 Issues

2017-12-06

maven-repository

This repository is a collection of artifacts with the gov.cdc group id for use in Java projects through the Maven build tool.

13 Forks

0 Issues

2018-04-16

HTML

MEBT

A Portfolio Website for the Molecular Epi and Bx Team

1 Forks

2 Issues

2019-05-15

1 Forks

0 Issues

2019-07-17

TypeScript

MicrobeTrace

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

32 Forks

154 Issues

2018-09-21

HTML

MicrobeTrace-Archive

Sequence analysis and data visualization tool

3 Forks

50 Issues

2017-06-27

2 Forks

5 Issues

2021-04-07

R

MicrobeTraceShiny

A little R package to Launch MicrobeTrace in a Shiny Server

1 Forks

1 Issues

2019-03-18

1 Forks

0 Issues

2017-09-29

0 Forks

0 Issues

2019-12-17

3 Forks

0 Issues

2017-09-29

0 Forks

1 Issues

2022-08-23

Shell

mycosnp

4 Forks

4 Issues

2021-02-24

mycosnp-bwa-pre-process

This workflow prepares and aligns samples using BWA for variant calling using the MycoSNP GATK workflow.

0 Forks

0 Issues

2021-02-24

mycosnp-bwa-reference

This workflow prepares a reference index using BWA as part of the MycoSNP suite of workflows.

1 Forks

0 Issues

2021-02-22

mycosnp-gatk-variants

This workflow calls variants for MycoSNP using GATK.

0 Forks

2 Issues

2021-02-24

Nextflow

mycosnp-nf

CDCgov/mycosnp-nf

15 Forks

16 Issues

2022-02-24

SAS

National-Vital-Statistics-Mortality-Data

Code for analyzing vital statistics mortality data, including death certificate literal text

2 Forks

0 Issues

2018-01-18

0 Forks

0 Issues

2022-11-18

0 Forks

0 Issues

2022-12-16

ncird_vsd_covid_vax_coverage_analysis

CDC Vaccine Safety Datalink COVID-19 Vaccination Coverage Among Persons 16 years and Older, Dec 2020-May 2021

1 Forks

0 Issues

2021-05-26

0 Forks

0 Issues

2022-09-01

NEDSS-DataIngestion

Data Ingestion for Modernization of NEDSS Project by Enquizit

0 Forks

0 Issues

2022-12-19

NEDSS-DataIngestionSandbox

Sandbox to test concepts and experiments without impacting the NEDSS-DataIngestion

0 Forks

0 Issues

2022-12-19

0 Forks

1 Issues

2022-10-19

0 Forks

1 Issues

2022-09-01

JavaScript

neighborjoining

Use Neighbor-Joining to turn distance matrices into phylogenetic trees in Browser and Node.js

1 Forks

0 Issues

2018-11-28

Jupyter Notebook

NeST

2 Forks

2 Issues

2020-07-07

NeST-nf

NeST NextFlow

3 Forks

0 Issues

2020-10-14

1 Forks

0 Issues

2021-08-05

0 Forks

0 Issues

2022-05-24

0 Forks

0 Issues

2020-08-07

HTML

NLPWorkbench

Natural Language processing for Pathology reports on cancer histology, laterality, side, and behavior.

10 Forks

1 Issues

2017-04-10

R

nncc

An R package that provides nearest-neighbors matching and analysis of case-control data.

0 Forks

0 Issues

2022-06-07

0 Forks

0 Issues

2022-08-16

Dockerfile

ocp-sonarqube

Version of the SonarQube container image that will run in the OpenShift restricted SCC.

1 Forks

0 Issues

2018-11-01

JavaScript

Ocra

A client-side webapp to scrape data from the standard Epidemiological Interview Record

2 Forks

0 Issues

2019-04-17

HTML

opencdc

This is the repository for the openCDC web site. Entire site is generated from data files describing CDC Open Technology types for data, api, code, and events. All CDC programs are welcome to submit pull requests with updates and new items useful to the public health open source community.

26 Forks

1 Issues

2018-08-08

40 Forks

5 Issues

2017-06-21

Python

Opioid_Involvement_NLP

Code to search clinical notes text for opioid involvement

0 Forks

0 Issues

2022-01-11

Python

Opioid_SUD_MHI_MedCodes

Code to flag ICD-10-CM codes related to opioid involvement, substance use disorder, and mental health issues in structured hospital data

0 Forks

0 Issues

2022-01-11

1 Forks

0 Issues

2020-12-02

HTML

patristic

A Phylogenetics toolkit for Javascript

3 Forks

5 Issues

2018-12-04

Python

phdi

0 Forks

7 Issues

2022-07-26

2 Forks

1 Issues

2022-09-28

Python

phdi-google-cloud

Terraform and Python code for deploying PHDI pipelines to Google Cloud Platform.

5 Forks

0 Issues

2022-07-26

JavaScript

phdi-site

0 Forks

0 Issues

2022-10-03

phin-vads-db

PHIN VADS Lite data

0 Forks

0 Issues

2017-05-03

1 Forks

0 Issues

2017-04-10

JavaScript

phlip

2 Forks

5 Issues

2020-03-28

1 Forks

2 Issues

2020-04-06

2 Forks

8 Issues

2020-04-06

Nextflow

phoenix

🔥🐦🔥PHoeNIx: A short-read pipeline for healthcare-associated and antimicrobial resistant pathogens

5 Forks

4 Issues

2022-05-10

HTML

PhysicsTree

A Radical Alternative to Conventional Phylogenetic Tree Renderers

2 Forks

3 Issues

2020-08-13

Kotlin

pid2fhir

Project for HL7 Dev Days 2019 Redmond. Converts V2 PIDs to FHIR Patient Resources

1 Forks

0 Issues

2019-06-07

HTML

pivotable

A simple, all-client-side web app to transform Adjacency lists into Edge Lists

1 Forks

3 Issues

2020-08-12

R

PooledInfRate

Functions for statistical estimation with pooled or grouped binary data

0 Forks

0 Issues

2022-03-30

PoSE

PoSE: (Pattern of Sequence Evolution) provides visualization and annotation of amino acid substitutions to help determine major patterns during sequence evolution of protein-coding sequences, hypervariable regions, or changes in dN/dS ratios.

2 Forks

2 Issues

2016-05-20

0 Forks

0 Issues

2021-05-17

0 Forks

0 Issues

2022-05-16

JavaScript

prime-central

2 Forks

1 Issues

2020-09-18

2 Forks

2 Issues

2020-10-07

2 Forks

43 Issues

2021-04-02

Rich Text Format

prime-field-teams

0 Forks

104 Issues

2021-02-11

HCL

prime-public-health-data-infrastructure

Repository for the joint CDC+USDS PRIME project's Data Ingestion prototype project. The goal is to work with raw vaccine, case, and lab report data to arrive at an analysis of breakthrough cases in the state of Virginia that uses a data lake as underlying storage.

3 Forks

2 Issues

2021-12-10

38 Forks

917 Issues

2020-10-15

Java

prime-simplereport

SimpleReport is a fast, free, and easy way for COVID-19 testing facilities to report results to public health departments.

17 Forks

305 Issues

2020-10-08

JavaScript

prime-simplereport-site

Landing / marketing site for the SimpleReport application

6 Forks

10 Issues

2020-11-17

JavaScript

Proximate

Pick a county, see its neighbors

1 Forks

0 Issues

2018-03-19

1 Forks

0 Issues

2017-09-29

JavaScript

react-starter-kit

Starter kit for use in creating new React projects

6 Forks

1 Issues

2020-09-14

1 Forks

0 Issues

2017-09-29

R

Rnssp

A Signature R package for the National Syndromic Surveillance Program (NSSP) at the Centers for Disease Control and Prevention (CDC). A collection of tools, functions, and R Markdown templates that supports the Community of Practice of the NSSP.

10 Forks

1 Issues

2021-05-20

R

Rnssp-rmd-templates

Rnssp R Markdown templates

6 Forks

1 Issues

2021-05-21

HTML

Rnssp-templates-docs

Online Documentation for Rnssp R Markdown Templates

4 Forks

0 Issues

2021-11-06

Shell

s2i-ruby-vocab-builder

Ruby Source-to-Image builder tailored to the needs of the SDP Vocabulary project.

1 Forks

0 Issues

2019-03-07

0 Forks

0 Issues

2022-06-10

Python

SanitizeMe

Remove host contaminants from sequencing files

3 Forks

0 Issues

2020-03-27

Python

SanitizeMePaired

Remove Host Reads from Paired End Sequencing

2 Forks

0 Issues

2020-04-03

Jupyter Notebook

SARS-CoV-2_FRNTcalculations

Jupyter Notebook file with R Script for FRNT50 Calculations from a folder of CSV files in 96-well plate format.

1 Forks

0 Issues

2021-09-08

7 Forks

0 Issues

2021-05-12

Perl

SARS-CoV-2_Sequencing

A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.

79 Forks

0 Issues

2020-03-18

R

savimpx

MPX Helper Functions for the Situational Awareness and Visualization Team

0 Forks

5 Issues

2022-07-11

R

SaviR

The purpose of SaviR is to collect the functions needed to access and prepare various COVID data sources.

8 Forks

4 Issues

2021-09-21

Nextflow

SC2CLIA

An SARS-CoV-2 bioinformatics pipeline for CLIA validation using Dr. Erin Young's Cecret StaphB pipeline as a base

1 Forks

1 Issues

2021-11-18

1 Forks

0 Issues

2017-09-29

Python

scraper

Python library for getting metadata from source code hosting tools

2 Forks

0 Issues

2019-03-01

Jinja

SDP

Repository for CDC's Surveillance Data Platform project.

6 Forks

0 Issues

2016-08-08

3 Forks

0 Issues

2017-04-10

1 Forks

0 Issues

2017-05-30

Smarty

SDP-Jenkins

Customized Jenkins Docker image for OpenShift using OCP Jenkins S2I builder

1 Forks

0 Issues

2017-12-12

R

SDP-MLaaS

Demonstrations of deploying machine learning models in R, MLflow, and ECPaaS

2 Forks

1 Issues

2019-08-21

SDP-Slide-Test

Repository for the SDP team to test slides.

1 Forks

0 Issues

2016-11-30

JavaScript

SDP-Vocabulary-Service

Repository for the SDP Vocabulary Service.

3 Forks

0 Issues

2016-09-19

Python

seqsender

Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories

5 Forks

2 Issues

2021-08-12

R

SeqSpawnR

Spawn Normally-Distributed Mutant DNA Sequences

1 Forks

1 Issues

2019-01-03

R

ShinyGanttCharts

Run Shiny. Make Gantt Charts.

2 Forks

0 Issues

2019-05-24

1 Forks

0 Issues

2020-08-24

R

snpeffr

R package for mycosnp-nf to parse outputs from snpeffr to desired formats for MDB/Fungi Net

0 Forks

0 Issues

2022-12-15

C#

Source-Code-Inventory

An application and Wiki for managing an inventory of source code, compliant with the Federal Source Code Policy.

4 Forks

0 Issues

2018-11-20

spheres-augur-build

This repository analyzes viral genomes using Nextstrain to understand how SARS-CoV-2, the virus that is responsible for the COVID-19 pandemic, evolves and spreads. This is a copy of the original Nextstrain ncov repository, which will (by default) build augur all 50 states + DC + PR using the same parameters and subsampling strategy.

8 Forks

2 Issues

2020-09-15

spheres-auspice-data

Data for the SPHERES Auspice site

1 Forks

0 Issues

2021-04-01

0 Forks

0 Issues

2022-04-27

HTML

springfox-swagger-ui

This is the repository extending the Springfox Swagger UI package to meet CDC browser requirements.

3 Forks

0 Issues

2018-04-06

Python

SUD_MHI_NLP

Code to flag mentions of substance use disorder and mental health issues in clinical note text

0 Forks

0 Issues

2022-01-11

0 Forks

0 Issues

2021-12-08

HTML

TableMerger

A little web tool to help people join data tables (without writing code!)

1 Forks

0 Issues

2019-07-29

R

TB_molecular_epidemiology

Algorithms for TB molecular epidemiology analysis

4 Forks

0 Issues

2019-01-17

template

Template repository with rules, practices, and privacy, license, records, notices to help programs use the CDCgov GitHub organization.

33 Forks

2 Issues

2016-02-17

0 Forks

0 Issues

2021-08-05

1 Forks

0 Issues

2017-02-25

0 Forks

0 Issues

2022-08-02

JavaScript

TidyTree

Uncompromisingly Flexible Phylogenetic Trees in Javascript

6 Forks

16 Issues

2019-01-14

Python

tn93

Tamura-Nei distance calculation

0 Forks

0 Issues

2022-08-16

JavaScript

tn93.js

Tamura-Nei '93 Computation in Javascript

2 Forks

2 Issues

2018-02-07

Shell

Tools

2 Forks

0 Issues

2018-03-28

Python

tostadas

🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission

1 Forks

0 Issues

2022-08-08

1 Forks

11 Issues

2022-09-28

Python

U50

U50 : measuring assembly output based on non-overlapping, target-specific contigs

3 Forks

0 Issues

2016-03-18

0 Forks

0 Issues

2021-11-03

0 Forks

0 Issues

2022-11-09

2 Forks

3 Issues

2020-06-30

2 Forks

0 Issues

2022-01-26

2 Forks

0 Issues

2017-01-11

1 Forks

0 Issues

2017-09-29