National Institute of Allergy and Infectious Diseases (NIAID)

All

155 repositories

image_portal_workflows
Public
Workflows related to project previously referred to as "Hedwig"
Python
•
BSD 3-Clause "New" or "Revised" License
•0•5•30•1•Updated Aug 28, 2025Aug 28, 2025
NCF1_variant_calling
Public
Variant calling pipeline, masking NCF1 pseudogenes
Python
•
MIT License
•0•0•0•0•Updated Aug 28, 2025Aug 28, 2025
terraform-aws-ssm-patch-manager
Public
Terraform module to provision AWS SSM Patch Manager maintenance window tasks, targets, patch baseline, patch groups and an s3 bucket for storing patch task logs
aws module terraform oeb-platform
HCL
•
Apache License 2.0
•18•0•0•5•Updated Aug 28, 2025Aug 28, 2025
monarch-actions-switch-account
Public
GitHub Action used to switch between Monarch Spaces accounts
module spaces monarch gha oeb-platform
TypeScript
•
MIT License
•0•1•1•6•Updated Aug 27, 2025Aug 27, 2025
tbp-cxr-outlier
Public
TB Portals Chest X-Ray Outlier Detector
Jupyter Notebook
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Apache License 2.0
•1•0•2•2•Updated Aug 25, 2025Aug 25, 2025
rap_sitkCore
Public
Common imaging utilities for RAP
Python
•
Apache License 2.0
•0•0•1•7•Updated Aug 24, 2025Aug 24, 2025
imaris_extensions
Public
Algorithmic and Utility Extensions for the Imaris Program
Python
•
Apache License 2.0
•3•18•2•0•Updated Aug 17, 2025Aug 17, 2025
sitk-ibex
Public
Aligning images acquired with the IBEX microscopy imaging technique
python microscopy image-registration
Python
•
Apache License 2.0
•6•17•1•1•Updated Aug 17, 2025Aug 17, 2025
tomojs-pytools
Public
hedwig niaid-hedwig niaid-hedwig-tomojs
Python
•3•3•3•4•Updated Aug 17, 2025Aug 17, 2025
neuroglancer
Public
WebGL-based viewer for volumetric data
niaid-hedwig
TypeScript
•
Apache License 2.0
•326•0•0•0•Updated Jul 31, 2025Jul 31, 2025
heterogeneity
Public
R
•0•0•0•0•Updated Jul 31, 2025Jul 31, 2025
puppeteer-sharp-test
Public
Headless Chrome .NET API
C#
•
MIT License
•475•0•0•4•Updated Jul 30, 2025Jul 30, 2025
terraform-aws-notify-slack
Public
Terraform module which creates SNS topic and Lambda function which sends notifications to Slack
slack module terraform oeb-platform
Python
•
Apache License 2.0
•347•0•0•1•Updated Jul 28, 2025Jul 28, 2025
Salmonella_superShedders
Public
Analysis code for salmonella super shedders project (Audrey Chong, Olivia Steele-Mortimer)
HTML
•0•0•0•0•Updated Jul 28, 2025Jul 28, 2025
JoesFlow
Public
R
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MIT License
•0•0•2•0•Updated Jul 24, 2025Jul 24, 2025
terraform-aws-managed-config-rules
Public
AWS Config Managed Rules Terraform Module
aws module terraform compliance aws-config aws-config-rules oeb-platform
HCL
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MIT License
•7•16•2•2•Updated Jul 21, 2025Jul 21, 2025
moleculer-netsparker-cloud
Public
Moleculer mixin for consuming Netsparker Cloud services.
back-end moleculer monarch oeb-platform
JavaScript
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MIT License
•0•1•0•1•Updated Jul 20, 2025Jul 20, 2025
shumi
Public
Pipeline to simulate HT-SGS datasets, from arbitrary RNA populations to CCS reads.
Python
•
MIT License
•0•1•0•0•Updated Jun 23, 2025Jun 23, 2025
monarch-actions-key-writer
Public
Monarch GitHub Action that installs SSH key to .ssh
module spaces gha monach oeb-platform
TypeScript
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MIT License
•94•0•0•5•Updated May 15, 2025May 15, 2025
dsb
Public
Normalize CITEseq Data
cite-seq niaid-tsang-lab
R
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Other
•13•66•6•0•Updated Apr 6, 2025Apr 6, 2025
metagenote
Public
Python
•2•3•0•0•Updated Mar 24, 2025Mar 24, 2025
UMI-pacbio-pipeline
Public
Pipeline to provide high accuracy single molecule consensus sequences from PacBio data using unique molecular identifiers (UMIs).
pacbio umi pacbio-data network-filtering unique-molecular-identifiers
Python
•
BSD 3-Clause "New" or "Revised" License
•2•6•0•0•Updated Feb 5, 2025Feb 5, 2025
workflow-application-token-action
Public
GitHub Action that will get a scoped short lived token for Actions workflows using a GitHub Application.
TypeScript
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MIT License
•50•0•0•0•Updated Jan 28, 2025Jan 28, 2025
monogenic-immune-health
Public
This repository consists of scripts and workflows used for generating results, figures, and tables published in the article: Rachel Sparks, Nicholas Rachmaninoff, William W. Lau, Dylan C. Hirsch, Neha Bansal, ..., John S. Tsang: A Unified Metric of Human Immune Health (Nature Medicine, 2024)
niaid-tsang-lab
HTML
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Other
•4•3•0•0•Updated Dec 9, 2024Dec 9, 2024
virome-pipeline
Public
This is a pipeline for exploring viruses (ssDNA, dsDNA phage, and giant DNA viruses) and viral diversity in metagenomes.
bioinformatics virus metagenomics bcbb-training
Python
•
MIT License
•0•12•0•0•Updated Nov 20, 2024Nov 20, 2024
niaid-design-system
Public
Welcome to the NIAID Design System.
design-system
Twig
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Other
•0•4•0•1•Updated Nov 6, 2024Nov 6, 2024
nbp_events_niaid
Public
0•0•0•0•Updated Oct 2, 2024Oct 2, 2024
2024_Introduction-to-R
Public
HTML
•2•2•0•0•Updated Sep 19, 2024Sep 19, 2024
fsc
Public
Code for: Integrating population and single-cell variations in vaccine responses identifies a naturally adjuvanted human immune setpoint
R
•1•2•0•0•Updated Sep 7, 2024Sep 7, 2024
ensembl-genomio
Public
Pipelines to turn basic genomic data into Ensembl cores and back
Python
•
Apache License 2.0
•9•0•0•0•Updated Sep 6, 2024Sep 6, 2024