Oregon Health and Science University Computational Biology

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213 repositories

scOPE
Public
scOPE learns mutation-linked expression programs from bulk RNA-seq and projects them into single-cell RNA-seq to infer per-cell mutation probabilities, revealin…
cancer-genomics copy-number-variation single-cell-rna-seq
cancer-genomics copy-number-variation single-cell-rna-seq mutation-signatures mutation-detection mutation-prediction
Jupyter Notebook
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MIT License
•0•1•0•0•Updated Mar 5, 2026Mar 5, 2026
UniVI
Public
UniVI is a scalable multi-modal VAE toolkit for aligning heterogeneous single-cell datasets into a shared latent space—supporting unimodal, dual-modal, and tri-…
deep-learning imputation data-analysis
deep-learning imputation data-analysis single-cell variational-autoencoders omics-data-integration mixture-of-experts data-denoising
Jupyter Notebook
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MIT License
•0•1•0•0•Updated Mar 4, 2026Mar 4, 2026
funnel
Public
Funnel is a toolkit for distributed task execution via a simple, standard API.
docker kubernetes google-cloud
docker kubernetes google-cloud slurm gridengine ga4gh aws-batch pbs-torque
Go
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MIT License
•42•137•131•12•Updated Mar 4, 2026Mar 4, 2026
embedding-kit
Public
Python
•3•1•0•1•Updated Mar 3, 2026Mar 3, 2026
helm-charts
Public
Helm Charts for deploying various projects in Kubernetes!
Go Template
•1•1•0•0•Updated Mar 2, 2026Mar 2, 2026
dpclust
Public
Dirichlet Process based methods for subclonal reconstruction of tumours
R
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GNU Affero General Public License v3.0
•19•0•0•1•Updated Feb 3, 2026Feb 3, 2026
battenberg
Public
Battenberg R package for subclonal copynumber estimation
R
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GNU Affero General Public License v3.0
•60•0•0•1•Updated Jan 30, 2026Jan 30, 2026
meeting-summarizer
Public
Summarizer for meeting transcripts
0•0•0•0•Updated Oct 15, 2025Oct 15, 2025
indexd
Public
Prototype index service server.
Python
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Apache License 2.0
•21•0•1•0•Updated Oct 14, 2025Oct 14, 2025
regulon-enrichment
Public
Jupyter Notebook
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GNU General Public License v3.0
•2•7•0•0•Updated Sep 2, 2025Sep 2, 2025
.github
Public template
0•0•0•0•Updated Aug 19, 2025Aug 19, 2025
fhir
Public
FHIR Protocol Buffers
C++
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Apache License 2.0
•202•0•0•0•Updated Aug 18, 2025Aug 18, 2025
homebrew-formula
Public
homebrew tap for OHSU Comp Bio tools
Ruby
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MIT License
•1•1•0•2•Updated Jul 12, 2025Jul 12, 2025
fence
Public
AuthN/AuthZ OIDC Service
Python
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Apache License 2.0
•49•0•1•0•Updated Jul 9, 2025Jul 9, 2025
indexclient
Public
Prototype index service client.
Python
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Apache License 2.0
•3•0•0•0•Updated Jul 9, 2025Jul 9, 2025
pypfb
Public
Python library & CLI to create, view and edit PFB files
Python
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Apache License 2.0
•13•0•0•0•Updated Jul 2, 2025Jul 2, 2025
gen3-workflow
Public
Gen3 service for GA4GH TES integration
Python
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Apache License 2.0
•1•1•0•0•Updated Jun 4, 2025Jun 4, 2025
funnel-plugins
Public
Golang Plugin development + testing using go-plugin from Hashicorp
bioinformatics authentication workflows
bioinformatics authentication workflows
Go
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Apache License 2.0
•2•1•0•1•Updated May 15, 2025May 15, 2025
compbio-galaxy-wrappers
Public archive
OHSU Galaxy wrappers.
Python
•10•6•0•0•Updated Apr 24, 2025Apr 24, 2025
py-tes
Public
Python SDK for the GA4GH Task Execution API
Python
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MIT License
•12•5•18•0•Updated Apr 9, 2025Apr 9, 2025
dpclust3p
Public
Dirichlet Process Clustering Pre-Processing Pipeline
R
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GNU Affero General Public License v3.0
•13•0•0•0•Updated Apr 4, 2025Apr 4, 2025
caliper-design
Public
Design docs for the CALIPER components and tools ⚙️
Apache License 2.0
•1•1•7•1•Updated Mar 26, 2025Mar 26, 2025
pycascades
Public
PyCascdes 2025 Demo
Python
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Apache License 2.0
•0•2•0•0•Updated Feb 9, 2025Feb 9, 2025
example-repo
Public
Test Repo!
HTML
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Apache License 2.0
•0•0•0•0•Updated Jan 31, 2025Jan 31, 2025
HTAN-FHIR
Public
python scripts to transform HTAN metadata to FHIR
Python
•0•0•0•0•Updated Jan 14, 2025Jan 14, 2025
fence-multipart
Public
AuthN/AuthZ OIDC Service
Python
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Apache License 2.0
•49•0•0•0•Updated Dec 9, 2024Dec 9, 2024
awesome-tes
Public
A curated list of awesome GA4GH TES projects and programs
workflow bioinformatics reproducible-research
workflow bioinformatics reproducible-research workflow-engine ga4gh
Creative Commons Zero v1.0 Universal
•0•2•1•0•Updated Dec 7, 2024Dec 7, 2024
vrs-annotator
Public
Annotates VCF Variants with VRS IDs
Jupyter Notebook
•2•2•0•0•Updated Nov 22, 2024Nov 22, 2024
syntheVAEiser
Public
Jupyter Notebook
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Apache License 2.0
•0•2•0•0•Updated Oct 18, 2024Oct 18, 2024
docker-centos-slurm
Public archive
Slurm Docker Container on CentOS 7
Shell
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MIT License
•4•0•0•0•Updated Oct 1, 2024Oct 1, 2024