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    20 repositories

    • ARIES

      Public
      Fast, accurate construction of multiple sequence alignments from protein language embeddings
      Python
      •
      MIT License
      •3•11•0•0•Updated Feb 20, 2026Feb 20, 2026

    • FBApro

      Public
      A linear-transformation based framework for integrating data with constraint based metabolic models
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Feb 4, 2026Feb 4, 2026

    • PathwayCCA

      Public
      PathwayCCA is a framework for pathway-level association analysis between multi-omic driver alterations and gene-set expression programs. The repository provides…
      Jupyter Notebook
      •0•0•0•0•Updated Dec 8, 2025Dec 8, 2025

    • kinaid

      Public
      KINAID Dashboard and library code
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 23, 2025Oct 23, 2025

    • bom-pooling

      Public
      Implementation of ISMB-25 Paper: Locality-aware pooling enhances protein language model performance across varied applications
      Python
      •0•6•0•0•Updated Aug 17, 2025Aug 17, 2025

    • Dyscovr

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated Dec 9, 2024Dec 9, 2024

    • optosos_supp_figures

      Public
      Code to generate supplementary figures for optos paper
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jul 26, 2024Jul 26, 2024

    • The-evolutionary-landscape-of-primate-protein-ligand-interfaces

      Public
      Python
      •0•1•0•0•Updated Aug 26, 2022Aug 26, 2022

    • Pou4_Misexpression

      Public
      All relevant code and results used in "Novel Neuronal Identities Derived by Misexpression of the POU IV Sensory Determinant in a Proto-Vertebrate". Chacha et al…
      PostScript
      •0•1•0•0•Updated Jan 29, 2022Jan 29, 2022

    • TandemDuplications

      Public
      Python
      •0•2•0•0•Updated Jan 5, 2022Jan 5, 2022

    • DeMaSk

      Public
      Prediction of protein substitution impact using a directional substitution matrix and homolog alignments
      Python
      •
      GNU General Public License v3.0
      •2•12•0•0•Updated Oct 25, 2021Oct 25, 2021

    • InteracDome

      Public
      Compute Site-Based Ligand-Binding Frequencies across the InteracDome
      Python
      •5•7•0•0•Updated Sep 22, 2021Sep 22, 2021

    • dSPRINT

      Public
      Per-position prediction of protein domains interaction-sites
      Python
      •2•6•0•0•Updated May 17, 2021May 17, 2021

    • run-hmmer

      Public
      Scripts to run both HMMER 2.3.2 and HMMER 3 on a set of Pfam HMMs, parse and combine results
      Python
      •1•0•0•0•Updated Sep 28, 2020Sep 28, 2020

    • diffASE

      Public
      differential allele-specific expression
      R
      •3•0•0•0•Updated Sep 2, 2020Sep 2, 2020

    • treeSim

      Public
      Simulates a Host and Guest Tree, and Sequences on top
      Python
      •1•1•0•0•Updated Sep 1, 2020Sep 1, 2020

    • PertInInt

      Public
      Rapidly uncover significantly somatically mutated protein functional regions
      Python
      •1•7•0•0•Updated Aug 17, 2020Aug 17, 2020

    • Differential-Mutation-Analysis

      Public
      Differential Mutation Analysis
      R
      •7•11•0•0•Updated May 24, 2020May 24, 2020

    • uKIN

      Public
      Using Knowledge In Networks
      Ruby
      •
      Other
      •0•3•0•0•Updated Apr 1, 2020Apr 1, 2020

    • nCOP

      Public
      Network-based coverage of mutational profiles
      Ruby
      •
      Other
      •1•3•0•0•Updated Sep 27, 2017Sep 27, 2017
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