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    74 repositories

    • htlv_integration_sites

      Public
      HTLV-1 integration site analysis notes and scripts
      R
      •
      MIT License
      •0•0•0•0•Updated Jan 31, 2025Jan 31, 2025

    • civic-v2

      Public
      CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer
      cancervariantscancer-genomicsbiocurationnci-itcrvariant-curation
      TypeScript
      •
      MIT License
      •5•21•67•9•Updated Jan 30, 2025Jan 30, 2025

    • civic-docs

      Public
      Source code for the civicdb.org docs
      civic
      Creative Commons Zero v1.0 Universal
      •8•5•19•1•Updated Jan 30, 2025Jan 30, 2025

    • pVACtools

      Public
      R
      •
      BSD 3-Clause Clear License
      •63•148•78•5•Updated Jan 30, 2025Jan 30, 2025

    • neoag_vaccine_scripts

      Public
      Python
      •0•0•12•0•Updated Jan 29, 2025Jan 29, 2025

    • pVACcompare

      Public
      JavaScript
      •0•0•0•0•Updated Jan 28, 2025Jan 28, 2025

    • docker-pvactools

      Public
      Python
      •
      Other
      •7•3•0•0•Updated Jan 17, 2025Jan 17, 2025

    • pVACtools_Intro_Course

      Public
      Getting started with pVACtools - pVACseq, pVACbind and pVACview
      CSS
      •
      Creative Commons Attribution 4.0 International
      •2•0•0•1•Updated Jan 10, 2025Jan 10, 2025

    • CIVIC_SVI_Course

      Public
      A hands on course explaining how to complete somatic cancer variant interpretation using CIViC and current guidelines
      CSS
      •
      Creative Commons Attribution 4.0 International
      •2•0•0•1•Updated Jan 10, 2025Jan 10, 2025

    • civicpy

      Public
      A python interface for the CIViC db application
      civic
      Python
      •
      MIT License
      •6•11•15•13•Updated Dec 19, 2024Dec 19, 2024

    • rnabio.org

      Public
      website for the rnaseq course
      SCSS
      •
      MIT License
      •38•95•19•2•Updated Dec 13, 2024Dec 13, 2024

    • pmbio.org

      Public
      Website for the precision medicine workshop
      SCSS
      •
      MIT License
      •22•44•13•1•Updated Nov 18, 2024Nov 18, 2024

    • docm

      Public archive
      Retired Project: Rails frontend to The Genome Institute's database of curated mutations (DoCM)
      Ruby
      •
      MIT License
      •5•5•6•0•Updated Oct 15, 2024Oct 15, 2024

    • bigmhc

      Public
      BigMHC predicts MHC-I (neo)epitope presentation and immunogenicity
      Jupyter Notebook
      •
      Other
      •10•0•0•0•Updated Oct 3, 2024Oct 3, 2024

    • VAtools

      Public
      A set of tools to annotate VCF files with expression and readcount data
      Python
      •
      MIT License
      •13•28•7•1•Updated Sep 3, 2024Sep 3, 2024

    • griffithlab.org

      Public
      Griffith lab research website
      JavaScript
      •
      MIT License
      •29•15•1•0•Updated Aug 24, 2024Aug 24, 2024

    • regtools

      Public
      Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.
      C++
      •
      MIT License
      •27•124•37•5•Updated Aug 21, 2024Aug 21, 2024

    • usp7_scripts

      Public
      Analysis collaboration with Albert Kim lab - impact of USP7 knockout on splicing
      R
      •
      MIT License
      •0•0•0•0•Updated Jul 16, 2024Jul 16, 2024

    • GenVisR

      Public
      Genome data visualizations
      R
      •
      Creative Commons Zero v1.0 Universal
      •63•214•60•4•Updated May 12, 2024May 12, 2024

    • DeepImmuno

      Public
      Deep-learning empowered prediction and generation of immunogenic epitopes for T cell immunity
      Jupyter Notebook
      •
      MIT License
      •26•2•0•0•Updated Mar 14, 2024Mar 14, 2024

    • civic-meeting

      Public
      Repo for advertising and organizing CIViC unconference/meeting activities
      civiccurationunconferencecivic-meetings
      3•10•13•0•Updated Mar 12, 2024Mar 12, 2024

    • Immuno_Workflow_Course

      Public
      CSS
      •
      MIT License
      •1•0•0•0•Updated Feb 8, 2024Feb 8, 2024

    • docker-vatools

      Public
      Dockerfile
      •1•0•0•0•Updated Feb 5, 2024Feb 5, 2024

    • civic-client

      Public
      Web client for CIViC: Clinical Interpretations of Variants in Cancer
      cancer-genomicsfront-end-frameworknci-itcrjavascriptciviccancervariants
      JavaScript
      •
      MIT License
      •28•50•230•13•Updated Nov 28, 2023Nov 28, 2023

    • civic-server

      Public
      Backend Server for CIViC Project
      cancervariantscancer-genomicsnci-itcrrubycivicbackend-server
      HTML
      •
      MIT License
      •32•39•52•13•Updated Jul 6, 2023Jul 6, 2023

    • genviz.org

      Public
      Genomic data interpretation and visualization Workshop
      SCSS
      •
      MIT License
      •4•19•14•5•Updated Jun 19, 2023Jun 19, 2023

    • DeepNeo

      Public
      identification of immunogenic neoepitopes
      Python
      •
      Other
      •5•0•0•0•Updated Jun 5, 2023Jun 5, 2023

    • rnaseq_tutorial

      Public
      Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.
      R
      •
      Other
      •619•1.4k•6•0•Updated May 31, 2023May 31, 2023

    • aml31

      Public
      Resource website for the AML31 publication
      CSS
      •1•2•0•0•Updated Mar 13, 2023Mar 13, 2023

    • anchor_huiming_etal_2023

      Public
      Code for computational workflows and analyses relating to "Computational prediction of MHC anchor locations guide neoantigen identification and prioritization"
      Jupyter Notebook
      •
      MIT License
      •0•6•0•0•Updated Feb 23, 2023Feb 23, 2023