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    50 repositories

    • TCRtoolkit

      Public
      A NextFlow pipeline for processing and analyzing TCRseq data
      Nextflow
      •
      MIT License
      •3•4•8•1•Updated Sep 10, 2026Sep 10, 2026

    • open-cravat-modules-karchinlab

      Public
      JavaScript
      •
      MIT License
      •11•2•1•6•Updated Sep 3, 2026Sep 3, 2026

    • probabilistic2020

      Public
      Simulates somatic mutations, and calls statistically significant oncogenes and tumor suppressor genes based on a randomization-based test
      bioinformaticscancersomatic-variants
      bioinformaticscancersomatic-variantsdriver-genesoncogenetumor-suppressor-gene
      Python
      •
      Apache License 2.0
      •5•8•2•2•Updated Sep 3, 2026Sep 3, 2026

    • CHASMplus

      Public
      Predicts which missense mutations will drive growth of human cancers
      Python
      •3•12•1•1•Updated Sep 2, 2026Sep 2, 2026

    • 2020plus

      Public
      Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests
      bioinformaticsrandom-forestcancer
      bioinformaticsrandom-forestcancersomatic-variantsdriver-genes
      Python
      •
      Apache License 2.0
      •17•50•9•1•Updated Sep 2, 2026Sep 2, 2026

    • HotMAPS_2016

      Public
      Detects hotspot regions for somatic mutations in 3D protein structures
      cancerprotein-structurehotspot
      cancerprotein-structurehotspotsomatic-mutationshotspot-regionsmissense-mutationsexome-scale
      Python
      •
      Apache License 2.0
      •0•3•5•0•Updated Sep 2, 2026Sep 2, 2026

    • open-cravat

      Public
      A modular annotation tool for genomic variants
      javascriptpythonbioinformatics
      javascriptpythonbioinformaticsgenomicspython3bioinformatics-pipelineannotation-toolvariant-annotationsvariant-annotationvariant-analysis
      JavaScript
      •
      MIT License
      •47•162•63•12•Updated Aug 29, 2026Aug 29, 2026

    • open-cravat-multiuser

      Public
      JavaScript
      •3•3•1•0•Updated Aug 24, 2026Aug 24, 2026

    • SVCFit

      Public
      R
      •
      Other
      •1•4•2•0•Updated Aug 4, 2026Aug 4, 2026

    • LibreChat

      Public
      Enhanced ChatGPT Clone: Features Agents, MCP, Skills, DeepSeek, Anthropic, AWS, OpenAI, Responses API, Azure, Groq, o1, GPT-5, Mistral, OpenRouter, Vertex AI, G…
      TypeScript
      •
      MIT License
      •8.9k•0•0•0•Updated Jul 24, 2026Jul 24, 2026

    • oc-mcp

      Public
      TypeScript
      •0•5•0•0•Updated Jul 15, 2026Jul 15, 2026

    • pictographPlus

      Public
      pictograph with copy number added
      R
      •
      MIT License
      •3•0•2•0•Updated Jul 8, 2026Jul 8, 2026

    • Public.Match

      Public
      Public Match project
      Python
      •1•1•0•0•Updated May 26, 2026May 26, 2026

    • CRAFT

      Public
      CRAFT: a generative transformer for embedding TCRβ repertoires and detecting immune perturbation
      Python
      •
      MIT License
      •0•2•0•0•Updated Apr 29, 2026Apr 29, 2026

    • open-cravat-readthedocs

      Public
      Python
      •5•1•1•1•Updated Apr 20, 2026Apr 20, 2026

    • pictographPlus-CCF_only

      Public
      pictographplus to estimate CCF only
      R
      •3•0•0•0•Updated Feb 23, 2026Feb 23, 2026

    • PICTographPlus_manuscript

      Public
      Scripts used for generating results in the PICTographPlus manuscript
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jan 14, 2026Jan 14, 2026

    • bigmhc

      Public
      BigMHC predicts MHC-I (neo)epitope presentation and immunogenicity
      Jupyter Notebook
      •
      Other
      •13•70•1•1•Updated Dec 17, 2025Dec 17, 2025

    • Do-Pseudoseqs-Matter

      Public
      Code and materials for the paper "Do Pseudosequences Matter in Neoantigen Prediction?"
      Jupyter Notebook
      •0•0•0•0•Updated Dec 9, 2025Dec 9, 2025

    • pictograph

      Public
      A Bayesian hierarchical model to build tumor evolutionary trees
      R
      •1•5•6•1•Updated Oct 25, 2025Oct 25, 2025

    • oc_vignettes

      Public
      JavaScript
      •0•0•0•0•Updated Aug 15, 2025Aug 15, 2025

    • mhcnuggets

      Public
      MHC Class I and Class II neoantigen binding prediction
      Python
      •
      Other
      •16•38•9•0•Updated Jul 23, 2025Jul 23, 2025

    • open-cravat-extras

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Jun 20, 2025Jun 20, 2025

    • SCHISM

      Public
      Subclonal Hierarchy Inference from Somatic Mutations
      Python
      •
      Other
      •9•21•5•1•Updated Feb 25, 2025Feb 25, 2025

    • open-cravat-roadmap

      Public
      0•0•8•0•Updated Oct 29, 2024Oct 29, 2024

    • Tokheim_Cell_Systems_2019

      Public
      Data analysis for the CHASMplus paper
      Jupyter Notebook
      •4•3•0•1•Updated Jun 3, 2024Jun 3, 2024

    • TCRtoolkit-SC

      Public
      A NextFlow pipeline to process, analyze, and visualize single cell TCRseq data
      Nextflow
      •0•0•0•0•Updated May 18, 2024May 18, 2024

    • open-cravat-dxapp

      Public
      open-cravat-dxapp
      Python
      •0•1•1•0•Updated May 6, 2024May 6, 2024

    • OC-cloudform

      Public
      Cloudformation templating for OpenCravat AWS pipeline with automated processing and upload to S3 bucket
      Python
      •1•0•0•0•Updated Feb 14, 2024Feb 14, 2024

    • HotMAPS

      Public
      Python
      •0•3•1•0•Updated Dec 29, 2023Dec 29, 2023
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