Repositories list

• 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•10•6•Updated Nov 15, 2024Nov 15, 2024

• geneplexus-app-v2

  Public
  GenePlexus App - backend (cloud functions) and frontend

  TypeScript

  •0•2•6•0•Updated Nov 15, 2024Nov 15, 2024

• .github

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•9•Updated Nov 1, 2024Nov 1, 2024

• pydab

  Public
  A _blazingly fast_ Python package for modifying and converting DAB files

  Python

  •

  MIT License

  •0•3•3•6•Updated Oct 29, 2024Oct 29, 2024

• PecanPy

  Public
  A fast, parallelized, memory efficient, and cache-optimized Python implementation of node2vec

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •22•156•15•6•Updated Oct 29, 2024Oct 29, 2024

• obnb

  Public
  A Python toolkit for setting up benchmarking dataset using biomedical networks

  machine-learningcomputational-biologybenchmark-datasets+ 1network-biology

  Python

  •

  MIT License

  •1•21•57•8•Updated Oct 29, 2024Oct 29, 2024

• txt2onto_prediction_workflow

  Public
  Finding public RNA-seq samples and studies related to the list of diseases requested by Lucas Gillenwater

  Python

  •0•0•0•0•Updated Oct 25, 2024Oct 25, 2024

• 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•0•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•23•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

  •1•1•0•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

  •3•11•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

• personalized_network_ML

  Public
  Build upon NOTMAD to build personalized network

  Jupyter Notebook

  •

  MIT License

  •3•0•0•0•Updated Nov 3, 2021Nov 3, 2021