Fred Hutch Data Science Lab

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151 repositories

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•55•1•Updated Aug 22, 2025Aug 22, 2025
bash_for_bio
Public
Reworking of the Bash for HPC book into a class format
TeX
•0•0•0•0•Updated Aug 19, 2025Aug 19, 2025
ITN_Workshops_2025
Public
An OTTR website for resources and activities for the ITN workshops at the ITCR Annual Meeting 2025
CSS
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MIT License
•0•0•2•0•Updated Aug 19, 2025Aug 19, 2025
ITN_course_search
Public
A searchable table for ITN courses
R
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MIT License
•0•0•1•1•Updated Aug 17, 2025Aug 17, 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•4•Updated Aug 13, 2025Aug 13, 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 privacy course risk hipaa data-sharing ethics de-identification itn-course audience-leaders
TeX
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Creative Commons Attribution 4.0 International
•0•1•13•2•Updated Aug 12, 2025Aug 12, 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•6•1•Updated Aug 12, 2025Aug 12, 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•13•28•1•Updated Aug 12, 2025Aug 12, 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 Aug 12, 2025Aug 12, 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•2•1•Updated Aug 12, 2025Aug 12, 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•1•Updated Aug 12, 2025Aug 12, 2025
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 Aug 8, 2025Aug 8, 2025
AnVIL_Poll_2024
Public
A summary of our findings from the 2024 State of the AnVIL user poll.
website anvil 2024 state-of-the-anvil user-poll
HTML
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MIT License
•0•0•4•1•Updated Aug 5, 2025Aug 5, 2025
Tools_for_Reproducible_Workflows_in_R
Public
CSS
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Creative Commons Attribution 4.0 International
•0•0•14•1•Updated Aug 1, 2025Aug 1, 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 Aug 1, 2025Aug 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 Aug 1, 2025Aug 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.
module epigenetics anvil ucsc-browser human-genomes course
CSS
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Creative Commons Attribution 4.0 International
•3•0•0•0•Updated Aug 1, 2025Aug 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 Aug 1, 2025Aug 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 Aug 1, 2025Aug 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 Aug 1, 2025Aug 1, 2025
AnVIL_SOTA_Polls
Public
An OTTR website for analyzing and reporting each year's State of the AnVIL Community Poll
R
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MIT License
•0•0•6•0•Updated Aug 1, 2025Aug 1, 2025
Clinical_Data_Management
Public
CSS
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MIT License
•1•0•6•3•Updated Aug 1, 2025Aug 1, 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 Aug 1, 2025Aug 1, 2025
DS-Resources
Public
CSS
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MIT License
•0•0•1•0•Updated Aug 1, 2025Aug 1, 2025
AnVIL_Outreach_Dashboard
Public
incomplete
CSS
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Creative Commons Attribution 4.0 International
•0•0•2•0•Updated Aug 1, 2025Aug 1, 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
•0•0•2•1•Updated Aug 1, 2025Aug 1, 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•6•1•Updated Aug 1, 2025Aug 1, 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•3•1•Updated Aug 1, 2025Aug 1, 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•1•4•1•Updated Aug 1, 2025Aug 1, 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•1•0•Updated Aug 1, 2025Aug 1, 2025