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    31 repositories

    • Seal

      Public
      Sequence-to-expression transfer learning framework for context-specific prediction of variant effects on expression
      Python
      •
      Other
      •0•1•0•0•Updated Apr 6, 2026Apr 6, 2026

    • humanbase-docs

      Public
      A template Sphinx repo
      1.1k•2•0•3•Updated Mar 31, 2026Mar 31, 2026

    • mahi

      Public
      AI framework for in silico genetic perturbation in tissue & cell-type context.
      Python
      •0•1•0•0•Updated Mar 18, 2026Mar 18, 2026

    • DaVinci-docs

      Public
      0•0•0•0•Updated Mar 7, 2026Mar 7, 2026

    • DaVinci

      Public
      Deconvolving lAtent Variables for Integrated Niche Cluster Identification
      R
      •1•1•0•1•Updated Mar 7, 2026Mar 7, 2026

    • otari

      Public
      code to run Otari and obtain Otari predictions
      Python
      •0•7•0•0•Updated Dec 17, 2025Dec 17, 2025

    • DIS

      Public
      Interpretable DIS+ AI framework for disease-specific variant pathogenicity
      Python
      •
      Other
      •0•1•0•0•Updated Dec 12, 2025Dec 12, 2025

    • otari-manuscript

      Public
      Code for reproducing the Otari manuscript results
      Python
      •0•0•0•0•Updated Nov 21, 2025Nov 21, 2025

    • hedgehog-framework

      Public
      code to run the Hedgehog methylation sequence model ML framework: training, evaluation, and prediction
      Python
      •
      Other
      •0•1•0•0•Updated Oct 30, 2025Oct 30, 2025

    • asd-pheno-classes

      Public
      Scripts to generate figures and data.
      Python
      •4•13•0•0•Updated Jul 15, 2025Jul 15, 2025

    • onboarding

      Public
      Information for new Troyanskaya lab members
      1•4•0•0•Updated Jun 13, 2025Jun 13, 2025

    • SPEEDI

      Public
      Single-cell Pipeline for End to End Data Integration (SPEEDI)
      non-commercial-license
      non-commercial-license
      R
      •0•4•1•0•Updated May 28, 2025May 28, 2025

    • ExPecto

      Public
      predicting expression effects of human genome variants ab initio from sequence
      Python
      •40•133•15•0•Updated Jan 28, 2025Jan 28, 2025

    • selene

      Public
      a framework for training sequence-level deep learning networks
      deep-learninggenomic-data-analysissampling-methods
      deep-learninggenomic-data-analysissampling-methods
      Jupyter Notebook
      •
      BSD 3-Clause Clear License
      •91•399•25•2•Updated Dec 16, 2024Dec 16, 2024

    • tapioca

      Public
      a framework for predicting global protein-protein interaction networks from dynamic mass spec data
      Python
      •
      BSD 3-Clause Clear License
      •1•24•1•1•Updated Mar 20, 2024Mar 20, 2024

    • find_website_network

      Public
      shiny app for FIND network visualization
      R
      •1•0•0•0•Updated Nov 2, 2023Nov 2, 2023

    • function

      Public
      Python library for functional genomics
      Python
      •
      GNU General Public License v3.0
      •4•4•0•2•Updated Jul 6, 2023Jul 6, 2023

    • sei-framework

      Public
      code to run sei and obtain sei and sequence class predictions
      Python
      •
      Other
      •10•113•13•0•Updated Dec 20, 2022Dec 20, 2022

    • sleipnir

      Public
      C++
      •
      Other
      •1•4•0•0•Updated Jul 11, 2022Jul 11, 2022

    • yenta

      Public
      Yet 'Nother Taskrunner
      Python
      •
      MIT License
      •1•0•0•0•Updated May 24, 2022May 24, 2022

    • sei-manuscript

      Public
      Code for reproducing the Sei manuscript results
      Jupyter Notebook
      •3•17•2•0•Updated Jan 25, 2022Jan 25, 2022

    • ketl

      Public
      konfigurable etl
      Python
      •
      MIT License
      •2•0•0•0•Updated Dec 21, 2021Dec 21, 2021

    • DeepArk

      Public
      Modeling the genomic regulatory codes of fly, mouse, worm, and fish with deep learning
      Python
      •
      BSD 3-Clause Clear License
      •3•17•1•0•Updated Apr 6, 2021Apr 6, 2021

    • HeartENN-models

      Public
      Documentation and scripts to run HeartENN (Richter et al., 2020)
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•3•0•0•Updated Dec 30, 2020Dec 30, 2020

    • flib

      Public
      Python
      •
      Other
      •2•1•0•0•Updated Nov 18, 2020Nov 18, 2020

    • dalliance

      Public
      Interactive web-based genome browser.
      JavaScript
      •
      BSD 2-Clause "Simplified" License
      •66•1•0•0•Updated May 13, 2019May 13, 2019

    • find_scripts

      Public
      Code for training ontology-based CRF model for tissue-developmental stage-specific gene prediction
      HTML
      •0•1•0•0•Updated Feb 22, 2019Feb 22, 2019

    • diseasequest-docker

      Public
      C++
      •2•3•2•0•Updated Apr 16, 2018Apr 16, 2018

    • giant-api-biojs

      Public archive
      BioJS connector for GIANT
      CSS
      •1•2•0•0•Updated Sep 22, 2017Sep 22, 2017

    • fntm-api

      Public
      Template code and documentation for FNTM API
      Python
      •0•0•0•0•Updated Jul 26, 2017Jul 26, 2017
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