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@krishnanlab

Krishnan Lab

Laboratory for Computational Genomics and Biomedical Data Science
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  1. PecanPy PecanPy Public

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

    Python 159 22

  2. txt2onto txt2onto Public

    Code for classifying unstructured text to tissue ontology terms using natural language processing and machine learning.

    Python 24 6

  3. teaching teaching Public

    Courses & workshops led by members of the Krishnan Lab.

    Jupyter Notebook 23 19

  4. obnb obnb Public

    A Python toolkit for setting up benchmarking dataset using biomedical networks

    Python 22 1

  5. PyGenePlexus PyGenePlexus Public

    A network based gene classification library to generate genome wide predictions about genes that are functionally similar to the input gene list.

    Python 20 3

  6. RNAseq_coexpression RNAseq_coexpression Public

    In-depth analysis of normalization and transformation methods for building coexpression networks from RNA-seq data.

    HTML 13 3

Repositories

Showing 10 of 37 repositories
  • PyGenePlexus Public

    A network based gene classification library to generate genome wide predictions about genes that are functionally similar to the input gene list.

    krishnanlab/PyGenePlexus’s past year of commit activity
    Python 20 3 16 4 Updated Feb 27, 2025
  • GSEAInContext-SemanticSimilarity Public

    Enhancing GSEA-InContext with Metadata-Based Study Similarity

    krishnanlab/GSEAInContext-SemanticSimilarity’s past year of commit activity
    0 0 0 0 Updated Feb 26, 2025
  • data_imbalance_project Public

    This repository contains code and analyses related to understanding and assessing the impact of class distributions on model predictions.

    krishnanlab/data_imbalance_project’s past year of commit activity
    Jupyter Notebook 0 1 0 1 Updated Feb 21, 2025
  • obnb Public

    A Python toolkit for setting up benchmarking dataset using biomedical networks

    krishnanlab/obnb’s past year of commit activity
    Python 22 MIT 1 60 7 Updated Feb 7, 2025
  • pydab Public

    A _blazingly fast_ Python package for modifying and converting DAB files

    krishnanlab/pydab’s past year of commit activity
    Python 3 MIT 0 3 6 Updated Feb 4, 2025
  • PecanPy Public

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

    krishnanlab/PecanPy’s past year of commit activity
    Python 159 BSD-3-Clause 22 15 (1 issue needs help) 6 Updated Feb 4, 2025
  • geneplexus-app-v2 Public

    GenePlexus App - backend (cloud functions) and frontend

    krishnanlab/geneplexus-app-v2’s past year of commit activity
    TypeScript 2 0 3 1 Updated Feb 2, 2025
  • .github Public
    krishnanlab/.github’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 12 Updated Feb 1, 2025
  • similarity_metrics_pipeline Public

    This repository contains tools and scripts for quantifying pairwise similarity between samples based on text descriptions

    krishnanlab/similarity_metrics_pipeline’s past year of commit activity
    0 1 0 2 Updated Dec 20, 2024
  • txt2onto_prediction_workflow Public

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

    krishnanlab/txt2onto_prediction_workflow’s past year of commit activity
    Python 0 0 0 0 Updated Dec 17, 2024
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