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@idekerlab

UC, San Diego Trey Ideker Lab

Bioinformatics software projects developed by UCSD Trey Ideker lab

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  1. DCell DCell Public

    DCell browser and gene deletion simulator

    JavaScript 123 34

  2. hiview hiview Public

    HiView: the universal viewer for hierarchical data

    JavaScript 16 7

  3. vizbi-2015 vizbi-2015 Public

    Sample data and notebooks for VIZBI 2015 tutorial session

    5 12

  4. Network_Evaluation_Tools Network_Evaluation_Tools Public

    Python 2.7 package with examples for evaluating a network's ability to group a given node set in network proximity.

    Jupyter Notebook 32 19

  5. pyNBS pyNBS Public

    Python 2.7 implementation of network-based stratification (NBS) algorithm from Hofree et al (Nature Methods 2013)

    Jupyter Notebook 37 22

Repositories

Showing 10 of 179 repositories
  • cellmaps_utils Public
    idekerlab/cellmaps_utils’s past year of commit activity
    Python 1 MIT 0 4 0 Updated Apr 10, 2025
  • agent_evaluation Public

    Supports papers on the development and evaluation of analyst and reviewer agents. Generate and evaluate mechanistic hypotheses derived from datasets.

    idekerlab/agent_evaluation’s past year of commit activity
    Jupyter Notebook 1 MIT 0 8 3 Updated Apr 9, 2025
  • cansrmapp Public
    idekerlab/cansrmapp’s past year of commit activity
    Python 0 0 0 0 Updated Apr 4, 2025
  • cookiecutter-musicpypackage Public
    idekerlab/cookiecutter-musicpypackage’s past year of commit activity
    Python 0 BSD-3-Clause 0 1 0 Updated Apr 1, 2025
  • G2PT Public
    idekerlab/G2PT’s past year of commit activity
    Jupyter Notebook 8 2 1 0 Updated Mar 26, 2025
  • cellmaps_pipeline Public
    idekerlab/cellmaps_pipeline’s past year of commit activity
    Python 4 MIT 0 0 0 Updated Mar 21, 2025
  • cellmaps_hierarchyeval Public

    Code for hierarchy evaluation

    idekerlab/cellmaps_hierarchyeval’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Mar 20, 2025
  • cellmaps_generate_hierarchy Public
    idekerlab/cellmaps_generate_hierarchy’s past year of commit activity
    Python 0 MIT 0 1 0 Updated Mar 19, 2025
  • cellmaps_coembedding Public
    idekerlab/cellmaps_coembedding’s past year of commit activity
    Python 0 MIT 1 1 0 Updated Mar 19, 2025
  • cellmaps_ppi_embedding Public
    idekerlab/cellmaps_ppi_embedding’s past year of commit activity
    Python 0 MIT 1 0 0 Updated Mar 19, 2025
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