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    35 repositories

    • .github

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•18•Updated Aug 1, 2025Aug 1, 2025

    • PecanPy

      Public
      A fast, parallelized, memory efficient, and cache-optimized Python implementation of node2vec
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •24•164•15•8•Updated Jul 31, 2025Jul 31, 2025

    • obnb

      Public
      A Python toolkit for setting up benchmarking dataset using biomedical networks
      machine-learningcomputational-biologybenchmark-datasetsnetwork-biology
      Python
      •
      MIT License
      •1•22•60•7•Updated Jul 28, 2025Jul 28, 2025

    • txt2onto_prediction_workflow

      Public
      Finding public RNA-seq samples and studies related to the list of diseases requested by Lucas Gillenwater
      Jupyter Notebook
      •0•0•0•1•Updated Jul 24, 2025Jul 24, 2025

    • multiomics-embedding

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jul 23, 2025Jul 23, 2025

    • PyGenePlexus

      Public
      A network based gene classification library to generate genome wide predictions about genes that are functionally similar to the input gene list.
      machine-learningbiological-networksgene-classification
      Python
      •
      Other
      •3•20•12•6•Updated Jul 16, 2025Jul 16, 2025

    • pydab

      Public
      A _blazingly fast_ Python package for modifying and converting DAB files
      Python
      •
      MIT License
      •0•3•3•6•Updated May 26, 2025May 26, 2025

    • geneplexus-app-v2

      Public
      GenePlexus App - backend (cloud functions) and frontend
      TypeScript
      •
      Other
      •0•2•4•0•Updated Apr 10, 2025Apr 10, 2025

    • txt2onto_predictions

      Public
      This repository, txt2onto_predictions, contains various predictions and analyses based on multiple requests from other researchers. The goal of this repository is to compile all the requested analyses in one place.
      0•0•0•0•Updated Sep 23, 2024Sep 23, 2024

    • cross-species-knowledge-transfer-paper-and-data

      Public
      Repo houses paper reviewed in cross species knowledge transfer paper and related data
      Apache License 2.0
      •0•0•0•0•Updated Aug 29, 2024Aug 29, 2024

    • microbiome-metadata-annotation

      Public
      Training text-based ML models to predict protocols for microbiome samples
      Jupyter Notebook
      •
      MIT License
      •0•3•0•0•Updated Aug 27, 2024Aug 27, 2024

    • txt2onto

      Public
      Code for classifying unstructured text to tissue ontology terms using natural language processing and machine learning.
      nlpannotationsomics-samples
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •6•25•2•1•Updated Aug 21, 2024Aug 21, 2024

    • Age-sex_signatures_in_humans_code

      Public
      code for Human pan-body age- and sex-specific molecular phenomena inferred from public transcriptome data using machine learning
      HTML
      •0•0•0•0•Updated Jul 10, 2024Jul 10, 2024

    • txt2onto2.0

      Public
      Public repo for txt2onto2.0
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•1•1•0•Updated Jun 18, 2024Jun 18, 2024

    • SNNomics

      Public
      Ranking the similarities of omics samples using siamese neural networks
      Python
      •
      MIT License
      •0•0•0•0•Updated May 8, 2024May 8, 2024

    • geneplexus_app

      Public
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•2•0•Updated Feb 13, 2024Feb 13, 2024

    • teaching

      Public
      Courses & workshops led by members of the Krishnan Lab.
      workshopsteachingcourses
      Jupyter Notebook
      •
      MIT License
      •19•23•0•0•Updated Feb 5, 2024Feb 5, 2024

    • GenePlexusZoo-Mancusript

      Public
      Repository Accompanying the manuscript J"oint representation of molecular networks from multiple species improves gene classification"
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•0•1•0•Updated Jan 20, 2024Jan 20, 2024

    • obnbench

      Public
      Benchmarking repository for OBNB
      Python
      •
      MIT License
      •0•2•0•0•Updated Dec 7, 2023Dec 7, 2023

    • gene-plexus

      Public
      WIP new gene plexus app
      0•0•0•0•Updated Nov 29, 2023Nov 29, 2023

    • gp-gcp-frontend

      Public
      This repo will test getting a GitHub page site talk to google cloud
      JavaScript
      •0•0•0•0•Updated Nov 3, 2023Nov 3, 2023

    • cone

      Public
      COntext-specific Network Embedding
      Python
      •
      MIT License
      •0•2•0•0•Updated Oct 30, 2023Oct 30, 2023

    • RNAseq_coexpression

      Public
      In-depth analysis of normalization and transformation methods for building coexpression networks from RNA-seq data.
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •4•15•2•0•Updated Aug 4, 2023Aug 4, 2023

    • NetworkLearningEval

      Public
      See https://github.com/krishnanlab/obnb
      MIT License
      •0•0•0•0•Updated Jun 8, 2023Jun 8, 2023

    • simplex

      Public
      Simplex app
      TypeScript
      •0•0•3•0•Updated Mar 22, 2023Mar 22, 2023

    • node2vecplus_benchmarks

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•0•0•Updated Jan 26, 2023Jan 26, 2023

    • chronic-inflammation

      Public
      Source code for "A network-based approach for isolating the chronic inflammation gene signatures underlying complex diseases towards finding new treatment opportunities"
      HTML
      •0•1•0•0•Updated Jul 21, 2022Jul 21, 2022

    • PecanPy_benchmarks

      Public
      Shell
      •
      BSD 3-Clause "New" or "Revised" License
      •0•6•0•0•Updated May 9, 2022May 9, 2022

    • GenePlexus

      Public
      Data, results, and code accompanying the manuscript: "Supervised learning is an accurate method for network-based gene classification"
      Python
      •
      Other
      •3•10•0•0•Updated Nov 3, 2021Nov 3, 2021

    • Expresto

      Public
      Data, results, and code accompanying the manuscript: "A Flexible, Interpretable, and Accurate Approach for Imputing the Expression of Unmeasured Genes" "
      Jupyter Notebook
      •
      Other
      •4•6•0•0•Updated Nov 3, 2021Nov 3, 2021