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@ylaboratory

ylaboratory

The home for scripts and tools developed by Vicky Yao's laboratory at the CS department at Rice University.

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  1. ETNA ETNA Public

    Embeddings to Network Alignment - align biological networks between two species

    Python 9 4

  2. splitpea splitpea Public

    A tool for calculating PPI network rewiring due to alternative splicing

    Jupyter Notebook 1 1

  3. flambe flambe Public

    datasets for tissue and tool named entity recognition, annotation files for biological workflow extraction, and disambiguation files

    Jupyter Notebook 4

  4. seismic seismic Public

    Seismic R package. Discover cell type-trait associations in minutes for GWAS and single-cell RNA-sequencing data

    R 13 4

Repositories

Showing 10 of 11 repositories
  • gene-embedding-benchmarks Public

    Benchmarking gene embeddings on single, paired, and gene set tasks

    ylaboratory/gene-embedding-benchmarks’s past year of commit activity
    Python 1 BSD-3-Clause 0 0 0 Updated Feb 2, 2025
  • seismic Public

    Seismic R package. Discover cell type-trait associations in minutes for GWAS and single-cell RNA-sequencing data

    ylaboratory/seismic’s past year of commit activity
    R 13 BSD-3-Clause 4 1 0 Updated Nov 28, 2024
  • ALPINE Public

    ALPINE is a semi-supervised non-negative matrix factorization (NMF) framework designed to effectively distinguish between multiple phenotypic conditions based on shared biological factors, while also providing direct interpretability of condition-associated genes.

    ylaboratory/ALPINE’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Nov 25, 2024
  • ANDES Public
    ylaboratory/ANDES’s past year of commit activity
    Jupyter Notebook 2 BSD-3-Clause 1 0 0 Updated Aug 28, 2024
  • flambe Public

    datasets for tissue and tool named entity recognition, annotation files for biological workflow extraction, and disambiguation files

    ylaboratory/flambe’s past year of commit activity
    Jupyter Notebook 4 CC-BY-4.0 0 0 0 Updated Jul 8, 2024
  • biomedical Public Forked from bigscience-workshop/biomedical

    Tools for curating biomedical training data for large-scale language modeling

    ylaboratory/biomedical’s past year of commit activity
    Python 1 116 0 0 Updated Jun 4, 2024
  • ar-biorxiv-style Public Forked from kourgeorge/arxiv-style

    A Latex style and template for paper preprints (based on NIPS style)

    ylaboratory/ar-biorxiv-style’s past year of commit activity
    TeX 0 MIT 325 0 0 Updated Mar 12, 2024
  • splitpea Public

    A tool for calculating PPI network rewiring due to alternative splicing

    ylaboratory/splitpea’s past year of commit activity
    Jupyter Notebook 1 BSD-3-Clause 1 0 0 Updated Jan 15, 2024
  • ETNA Public

    Embeddings to Network Alignment - align biological networks between two species

    ylaboratory/ETNA’s past year of commit activity
    Python 9 BSD-3-Clause 4 0 1 Updated Sep 8, 2023
  • kraken2 Public Forked from DerrickWood/kraken2

    The second version of the Kraken taxonomic sequence classification system

    ylaboratory/kraken2’s past year of commit activity
    C++ 0 MIT 275 0 0 Updated Jun 1, 2021
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