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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 124 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 182 repositories
  • cellmaps_vnn Public
    idekerlab/cellmaps_vnn’s past year of commit activity
    Python 0 MIT 2 1 0 Updated Oct 28, 2025
  • cellmaps_coembedding Public
    idekerlab/cellmaps_coembedding’s past year of commit activity
    Python 0 MIT 2 1 0 Updated Oct 23, 2025
  • csn_vnni Public

    Interpretable neural network for predicting drug responses and deciphering the effect of specific genetic alterations on sensitivity and resistance

    idekerlab/csn_vnni’s past year of commit activity
    Python 0 0 0 0 Updated Oct 10, 2025
  • cellmaps_generate_hierarchy Public
    idekerlab/cellmaps_generate_hierarchy’s past year of commit activity
    Python 0 MIT 2 1 0 Updated Oct 8, 2025
  • hit_map Public
    idekerlab/hit_map’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Sep 22, 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 2 MIT 1 8 3 Updated Sep 18, 2025
  • cellmaps_pipeline Public
    idekerlab/cellmaps_pipeline’s past year of commit activity
    Python 12 MIT 2 0 0 Updated Aug 19, 2025
  • MutationProjector Public

    Source code for MutationProjector

    idekerlab/MutationProjector’s past year of commit activity
    Python 1 MIT 0 0 0 Updated Aug 14, 2025
  • G2PT Public
    idekerlab/G2PT’s past year of commit activity
    Jupyter Notebook 19 MIT 5 3 0 Updated Aug 13, 2025
  • cellmaps_hierarchyeval Public

    Code for hierarchy evaluation

    idekerlab/cellmaps_hierarchyeval’s past year of commit activity
    Python 0 MIT 1 0 0 Updated Jul 25, 2025
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