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    39 repositories

    • pydab

      Public
      A _blazingly fast_ Python package for modifying and converting DAB files
      Python
      •
      MIT License
      •0•3•3•6•Updated Sep 28, 2026Sep 28, 2026

    • obnb

      Public
      A Python toolkit for setting up benchmarking dataset using biomedical networks
      machine-learningcomputational-biologybenchmark-datasets
      machine-learningcomputational-biologybenchmark-datasetsnetwork-biology
      Python
      •
      MIT License
      •2•22•60•7•Updated Sep 28, 2026Sep 28, 2026

    • ModGenePlexus

      Public
      Code to recreate study biased holdout for ModGenePlexus
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Sep 24, 2026Sep 24, 2026

    • meta2onto

      Public
      Frontend and backend for the meta2onto project
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•1•1•Updated Sep 24, 2026Sep 24, 2026

    • multiomics-embedding

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Sep 23, 2026Sep 23, 2026

    • meta-hq

      Public
      A platform for harmonizing and distributing community-curated high-quality metadata of public omics samples and datasets.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•8•0•Updated Sep 11, 2026Sep 11, 2026

    • 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
      machine-learningbiological-networksgene-classification
      Python
      •
      Other
      •3•21•4•7•Updated Aug 17, 2026Aug 17, 2026

    • PecanPy

      Public
      A fast, parallelized, memory efficient, and cache-optimized Python implementation of node2vec
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •25•176•17•8•Updated Jul 13, 2026Jul 13, 2026

    • dis-sex-imbalance

      Public
      Public repo for sex metadata imbalance project
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Jul 13, 2026Jul 13, 2026

    • .github

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•26•Updated Jun 1, 2026Jun 1, 2026

    • icepop

      Public
      public repo for icepop
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated May 12, 2026May 12, 2026

    • icepop_analysis

      Public
      Reproduce of results from ICePop paper
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated May 12, 2026May 12, 2026

    • teaching

      Public
      Courses & workshops led by members of the Krishnan Lab.
      workshopsteachingcourses
      workshopsteachingcourses
      Jupyter Notebook
      •
      MIT License
      •19•24•0•0•Updated Sep 7, 2025Sep 7, 2025

    • geneplexus-app

      Public
      GenePlexus App - backend (cloud functions) and frontend
      TypeScript
      •
      Other
      •0•1•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 …
      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•5•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
      nlpannotationsomics-samples
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •7•28•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
      •5•3•1•0•Updated Jun 18, 2024Jun 18, 2024

    • SNNomics

      Public
      Ranking the similarities of omics samples using siamese neural networks
      Python
      •
      MIT License
      •0•1•0•0•Updated May 8, 2024May 8, 2024

    • geneplexus-app-old

      Public
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•2•0•Updated Feb 13, 2024Feb 13, 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
      •1•2•0•0•Updated Dec 7, 2023Dec 7, 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•5•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
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