Fred Hutch Data Science Lab

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128 repositories

AnVIL_Collection
Public
📚 An auto-generating collection of all materials related to the AnVIL and GDSCN projects
website anvil content-library gdscn edtech-software
R
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Creative Commons Attribution 4.0 International
•1•0•4•1•Updated Jan 19, 2025Jan 19, 2025
AnVIL_Outreach_Dashboard
Public
incomplete
CSS
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Creative Commons Attribution 4.0 International
•0•0•4•1•Updated Jan 19, 2025Jan 19, 2025
spatialTIME
Public
R
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Other
•5•0•0•0•Updated Jan 18, 2025Jan 18, 2025
ITN_moffitt_2025
Public
Website with workshop information and activities for ITN workshops at Moffitt Feb 2025
itn-workshop
CSS
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MIT License
•0•0•3•0•Updated Jan 17, 2025Jan 17, 2025
AnVIL_Demos
Public
⏱ 30-minute demos and tutorials from our live AnVIL series
cloud course research module genomics cloud-computing anvil
CSS
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Creative Commons Attribution 4.0 International
•1•0•5•0•Updated Jan 15, 2025Jan 15, 2025
GDSCN_SARS_RStudio_on_AnVIL
Public
Lab module and lectures for identifying phylogenetic history of SARS variants using R
course module anvil phylogenetic-analysis sars-cov-2 gdscn
CSS
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Creative Commons Attribution 4.0 International
•0•0•6•1•Updated Jan 15, 2025Jan 15, 2025
GDSCN_BioDIGS_Book
Public
Getting started guide for using BioDIGS data in the classroom. Includes general information about BioDIGS.
tutorial course anvil r-programming gdscn biodigs
CSS
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Creative Commons Attribution 4.0 International
•0•0•1•2•Updated Jan 15, 2025Jan 15, 2025
GDSCN_BioDIGS_AMR
Public
This is a BioDIGS in the Classroom companion guide for the BioDIGS project. This particular activity guides students through an investigation of antimicrobial resistance in the BioDIGS samples using Galaxy.
course module gdscn biodigs
CSS
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Creative Commons Attribution 4.0 International
•0•0•2•1•Updated Jan 15, 2025Jan 15, 2025
GDSCN_BioDIGS_Soil
Public
This is a BioDIGS in the Classroom companion guide for the BioDIGS project. This particular activity guides students through exploration and visualization of the soil characteristics data using R.
course module anvil gdscn biodigs
CSS
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Creative Commons Attribution 4.0 International
•0•0•5•1•Updated Jan 15, 2025Jan 15, 2025
AnVIL_Urban_Genomics_PCA
Public
Lab module and lectures for exploring PCA using feral pigeon populations
course genomics pca anvil urban-data-science
CSS
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Creative Commons Attribution 4.0 International
•1•0•5•1•Updated Jan 15, 2025Jan 15, 2025
AnVIL_SRA_Data
Public
Pull Sequence Read Archive (SRA) data into AnVIL
course module genomics anvil ncbi-database sequence-read-archive
CSS
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Creative Commons Attribution 4.0 International
•0•0•6•1•Updated Jan 15, 2025Jan 15, 2025
AnVIL_Book_Epigenetics_Intro
Public
An introductory activity for epigenetics, or the idea of "nature versus nurture" in genetics. Learners use the UCSC Genome Browser.
module epigenetics anvil ucsc-browser human-genomes course
CSS
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Creative Commons Attribution 4.0 International
•3•0•6•1•Updated Jan 15, 2025Jan 15, 2025
AnVIL_Researcher_Journey
Public
CSS
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Creative Commons Attribution 4.0 International
•0•0•5•1•Updated Jan 15, 2025Jan 15, 2025
AnVIL_Data_Subsetting
Public
Tutorial for running the fastq_subsample WDL workflow on AnVIL!
workflow course module genomics wdl anvil wdl-workflow
CSS
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Creative Commons Attribution 4.0 International
•0•0•0•1•Updated Jan 15, 2025Jan 15, 2025
Intermediate_Python
Public
CSS
•0•0•0•0•Updated Jan 14, 2025Jan 14, 2025
OTTR_Quarto_Website
Public template
OTTR template for making a Quarto based website
CSS
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MIT License
•0•0•1•0•Updated Jan 14, 2025Jan 14, 2025
AI_for_Decision_Makers
Public
This set of four mini courses helps leaders make strategic decisions, drive innovation, enhance efficiency, and foster a culture that embraces the transformative power of these technologies.
course ai regulations hutch-course itn-course audience-leaders category-fundamentals-tools-resources using-ai ai-tasks avoiding-harm
TeX
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Creative Commons Attribution 4.0 International
•1•1•20•3•Updated Jan 10, 2025Jan 10, 2025
GitHub_Automation_for_Scientists
Public
This course walks through why's and the how's for using automation to boost scientific software development process.
automation templates activities troubleshooting github-actions itn-course audience-software-developers category-software-dev
CSS
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Creative Commons Attribution 4.0 International
•1•1•5•3•Updated Jan 10, 2025Jan 10, 2025
Choosing_Genomics_Tools
Public
Based on their genomic data types and goals, this course will help learners find educational resources and tools to help them process and interpret data.
data-processing genomic-data data-interpretation itn-course audience-researchers category-fundamentals-tools-resources resources-and-tools
TeX
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Creative Commons Attribution 4.0 International
•6•8•27•3•Updated Jan 10, 2025Jan 10, 2025
Containers_for_Scientists
Public
A course to introduce Docker for research purposes
docker containers itn-course future-course
CSS
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Creative Commons Attribution 4.0 International
•1•1•0•2•Updated Jan 10, 2025Jan 10, 2025
Intro_to_Python
Public
The course covers fundamentals of Python, a high-level programming language, and use it to wrangle data for analysis and visualization.
hutch-course
JavaScript
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Creative Commons Attribution 4.0 International
•0•0•1•1•Updated Jan 10, 2025Jan 10, 2025
Tools_for_Reproducible_Workflows_in_R
Public
CSS
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Creative Commons Attribution 4.0 International
•0•0•12•1•Updated Jan 10, 2025Jan 10, 2025
DataViz_Practice
Public
ITN course "Cancer Informatics Data Visualization in Practice" focusing on practicing best practices in data visualization
CSS
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Creative Commons Attribution 4.0 International
•0•0•4•2•Updated Jan 10, 2025Jan 10, 2025
DataViz_Considerations
Public
ITN course "Considerations for Bioinformatic Data Visualization" focusing on considerations for best practices in data visualization
CSS
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Creative Commons Attribution 4.0 International
•0•0•4•2•Updated Jan 10, 2025Jan 10, 2025
Intermediate_R
Public
The course continues building programming fundamentals in R programming and data analysis. You will learn how to make use of complex data structures, use custom functions built by other R users, creating your own functions, and how to iterate repeated tasks that scales naturally.
hutch-course
JavaScript
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Creative Commons Attribution 4.0 International
•0•0•4•1•Updated Jan 10, 2025Jan 10, 2025
Ethical_Data_Handling_for_Cancer_Research
Public
This course is designed to help researchers and investigators understand the key principles of data management from an ethics, privacy, security, usability and discoverability perspective.
security data privacy research risk hipaa data-sharing ethics phi pii
TeX
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Creative Commons Attribution 4.0 International
•0•1•13•3•Updated Jan 10, 2025Jan 10, 2025
AI_for_Efficient_Programming
Public
This course on AI for software development explores the use of AI large language models (ChatGPT, Bard, etc) and their potential benefits and challenges. Hands-on activities show the ways in which AI can speed up software development tasks and free up time for more creative and strategic work, maximizing benefits/efficiency while limiting harm.
course chatbot artificial-intelligence ethics learn-ai llm llms software-learning hutch-course itn-course
CSS
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Creative Commons Attribution 4.0 International
•1•3•11•3•Updated Jan 10, 2025Jan 10, 2025
OTTR_Quarto
Public template
Repo for Quarto based Open-source Tools for Training Resources (OTTR)
quarto quarto-template
CSS
•1•2•7•1•Updated Jan 10, 2025Jan 10, 2025
bench_to_bytes
Public
A guide for wet bench researchers about why considering computational and data science skills can be useful for all types of scientific work.
CSS
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Creative Commons Attribution 4.0 International
•0•0•5•5•Updated Jan 10, 2025Jan 10, 2025
Intermediate-Git-GitHub
Public
You will expand your current knowledge of Git and GitHub to help your research be more collaborative, reproducible, and transparent.
hutch-course
JavaScript
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Creative Commons Attribution 4.0 International
•0•0•4•1•Updated Jan 10, 2025Jan 10, 2025