Pinned Repositories
3Dmodel_scripts
This repository contains the custom scripts used in the automated workflows hosted on the NIH 3D Print Exchange (3dprint.nih.gov).
baseline
Reproducible workflows for the data analysis of "Baseline" project
covid19-time-resolved
This repository consists of scripts and workflows used for generating results, figures, and tables published in the article: Can Liu, Andrew J. Martins, William W. Lau, Nicholas Rachmaninoff, ..., John S. Tsang. "Time-resolved Systems Immunology Reveals a Late Juncture Linked to Fatal COVID-19" Cell (2021), In press.
dsb
Normalize CITEseq Data
imaris_extensions
Algorithmic and Utility Extensions for the Imaris Program
Nephele
Nephele Pipeline Scripts
python_biologist
Python Programming for Biologists
R_Intro
A Gentle Introduction to R, RStudio, and visualization
sitk-ibex
Aligning images acquired with the IBEX microscopy imaging technique
terraform-aws-managed-config-rules
AWS Config Managed Rules Terraform Module
National Institute of Allergy and Infectious Diseases (NIAID)'s Repositories
niaid/sitk-ibex
Aligning images acquired with the IBEX microscopy imaging technique
niaid/imaris_extensions
Algorithmic and Utility Extensions for the Imaris Program
niaid/terraform-aws-managed-config-rules
AWS Config Managed Rules Terraform Module
niaid/virome-pipeline
This is a pipeline for exploring viruses (ssDNA, dsDNA phage, and giant DNA viruses) and viral diversity in metagenomes.
niaid/UMI-pacbio-pipeline
Pipeline to provide high accuracy single molecule consensus sequences from PacBio data using unique molecular identifiers (UMIs).
niaid/image_portal_workflows
Workflows related to project previously referred to as "Hedwig"
niaid/niaid-design-system
Welcome to the NIAID Design System.
niaid/monogenic-immune-health
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/tomojs-pytools
niaid/2024_Introduction-to-R
niaid/dicom2stl
niaid/AMI_2024_Examples
Code Examples for Kristen Browne's Talk at Association of Medical Illustrators 2024 conference.
niaid/monarch-actions-switch-account
GitHub Action used to switch between Monarch Spaces accounts
niaid/fsc
Code for: Integrating population and single-cell variations in vaccine responses identifies a naturally adjuvanted human immune setpoint
niaid/monarch-actions-key-writer
Monarch GitHub Action that installs SSH key to .ssh
niaid/nbp_events_niaid
niaid/ApiCommonData
niaid/ensembl-genomio
Pipelines to turn basic genomic data into Ensembl cores and back
niaid/GusAppFramework
niaid/GusSchema
niaid/JoesFlow
niaid/LabKeytutorialModules
Example modules used for demos and tutorials
niaid/meshconvert
niaid/rap_sitkCore
Common imaging utilities for RAP
niaid/ReFlow
niaid/retired
Products in this repository have been retired, but have been made available. They are no longer maintained by NIAID. If they have been implemented elsewhere, a link will be provided.
niaid/tbp-cxr-outlier
TB Portals Chest X-Ray Outlier Detector
niaid/terraform-aws-notify-slack
Terraform module which creates SNS topic and Lambda function which sends notifications to Slack
niaid/terraform-aws-ssm-patch-manager
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
niaid/TuningManager