Fred Hutch Data Science Lab

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158 repositories

reproducibility_capstone
Public
A capstone course for the ITN Reproducibility Series with hands-on activities
docker reproducible-research reproducibility workflow-automation capstone-project github-secrets github-actions itn-course audience-researchers audience-software-developers
CSS
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Creative Commons Attribution 4.0 International
•0•0•3•0•Updated Oct 31, 2025Oct 31, 2025
AnVIL_Outreach_Dashboard
Public
incomplete
CSS
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Creative Commons Attribution 4.0 International
•0•0•2•0•Updated Oct 31, 2025Oct 31, 2025
intro_to_sql
Public
Intro to SQL Course for Fred Hutch
HTML
•1•6•0•0•Updated Oct 31, 2025Oct 31, 2025
ITN_Surveys
Public
Store Surveys for ITN
R
•0•0•0•0•Updated Oct 30, 2025Oct 30, 2025
GEMs
Public
💎 Materials & Portal for the Genomics Education Modules (GEMs) Program at Fred Hutch
education bioinformatics genomics entry-level entry-level-bioinformatics
TeX
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MIT License
•0•0•58•2•Updated Oct 30, 2025Oct 30, 2025
SOTA2024_ReportOut
Public
Materials associated with the Report Out for the State of the AnVIL 2024
HTML
•0•0•3•1•Updated Oct 29, 2025Oct 29, 2025
gems_surveys
Public
A collection of surveys for GEMs
R
•0•0•0•0•Updated Oct 29, 2025Oct 29, 2025
Proactive_Data_Management_and_Sharing
Public
Data management and sharing best practices for biomedical data handling folks
security privacy course reproducible-research reproducible-science data-management reproducibility hipaa data-sharing audience-leaders
TeX
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Creative Commons Attribution 4.0 International
•0•0•1•0•Updated Oct 28, 2025Oct 28, 2025
ITN_course_search
Public
A searchable table for ITN courses
search-tool itn
R
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MIT License
•0•0•1•1•Updated Oct 27, 2025Oct 27, 2025
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•1•1•Updated Oct 26, 2025Oct 26, 2025
DaSEH
Public
🌼 Collection of materials to accompany the R25 funded "Data Science for Environmental Health" short course
data-science course tidyverse public-health beginner beginner-friendly r-programming niehs environmental-health beginner-programming
HTML
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MIT License
•1•2•21•3•Updated Oct 22, 2025Oct 22, 2025
daseh_instructor_guide
Public
CSS
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Creative Commons Attribution 4.0 International
•0•0•6•0•Updated Oct 21, 2025Oct 21, 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.
course data-processing genomic-data data-interpretation itn-course audience-researchers category-fundamentals-tools-resources resources-and-tools launched-aug2023
TeX
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Creative Commons Attribution 4.0 International
•7•15•29•1•Updated Oct 21, 2025Oct 21, 2025
microbiome-poll
Public
HTML
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MIT License
•0•0•0•0•Updated Oct 17, 2025Oct 17, 2025
daseh_surveys
Public
HTML
•0•0•0•0•Updated Oct 17, 2025Oct 17, 2025
Containers_for_Scientists
Public
This course covers how to use containers for scientific software development. Scientific software benefits from the concepts of continuous integration (CI) and continuous deployment (CD). Containers play a critical role in CI/CD by providing a consistent, portable, and isolated environment for building, testing, and deploying software.
docker course containers ci-cd software itn-course audience-software-developers category-software-dev launched-nov2024 reproducibility-series-iv
CSS
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Creative Commons Attribution 4.0 International
•2•1•3•1•Updated Oct 16, 2025Oct 16, 2025
Intro_to_R
Public
The course covers fundamentals of R, a high-level programming language, and use it to wrangle data for analysis and visualization. The programming skills you will learn are transferable to learn more about R independently and other high-level languages such as Python.
hutch-course
HTML
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Creative Commons Attribution 4.0 International
•0•1•6•1•Updated Oct 15, 2025Oct 15, 2025
Machine-Learning
Public
CSS
•0•0•0•0•Updated Oct 13, 2025Oct 13, 2025
code_4_pub
Public
Workshop on Making Code Ready for Publication
0•0•0•0•Updated Oct 13, 2025Oct 13, 2025
bash_for_bio
Public
Reworking of the Bash for HPC book into a class format
TeX
•1•1•0•0•Updated Oct 9, 2025Oct 9, 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 course templates activities troubleshooting github-actions itn-course audience-software-developers category-software-dev launched-nov2023
CSS
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Creative Commons Attribution 4.0 International
•2•1•4•3•Updated Oct 2, 2025Oct 2, 2025
FH_Cluster_101
Public
This course introduces users to the Fred Hutch Cluster. It will lead users through account creation, using the terminal, connecting to the cluster, submitting jobs, and transferring files. Available in both web and Leanpub formats.
course command-line hpcc computing-cluster hutch-course
JavaScript
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Creative Commons Attribution 4.0 International
•2•0•8•1•Updated Oct 2, 2025Oct 2, 2025
Overleaf_and_LaTeX_for_Scientific_Articles
Public
This course is designed to help researchers and trainees write scientific articles using LaTeX and Overleaf.
course latex templates typesetting collaboration overleaf arxiv scientific-publications getting-help itn-course
CSS
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Creative Commons Attribution 4.0 International
•0•1•3•1•Updated Oct 2, 2025Oct 2, 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•3•0•Updated Oct 1, 2025Oct 1, 2025
test_bench_to_bytes
Public
Dummy repo created to help figure out https://github.com/fhdsl/bench_to_bytes/issues/7
CSS
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Creative Commons Attribution 4.0 International
•0•0•4•0•Updated Oct 1, 2025Oct 1, 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.
course module epigenetics anvil ucsc-browser human-genomes
CSS
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Creative Commons Attribution 4.0 International
•3•0•0•0•Updated Oct 1, 2025Oct 1, 2025
fhdsl_Training_Kit
Public
This resource is intended to provide guidance and assistance for creating online and in-person training materials.
CSS
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Creative Commons Attribution 4.0 International
•0•0•4•0•Updated Oct 1, 2025Oct 1, 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 Oct 1, 2025Oct 1, 2025
NIH_Data_Sharing
Public
Learn about the new NIH data sharing policy, places where you might want to share your particular kind of data, and how to deal with possible challenges associated with the policy.
data-storage policy budgeting data-management data-sharing nih grant-proposals grant-submission hutch-course itn-course
CSS
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Creative Commons Attribution 4.0 International
•0•0•7•1•Updated Oct 1, 2025Oct 1, 2025
Robust_Software_Development
Public
ITN course on robust software development and giving your code base a full set of features beyond the code itself
CSS
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Creative Commons Attribution 4.0 International
•0•0•4•0•Updated Oct 1, 2025Oct 1, 2025