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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 10 5

  2. flambe flambe Public

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

    Jupyter Notebook 6 1

  3. seismic seismic Public

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

    R 56 9

  4. gene-embedding-benchmarks gene-embedding-benchmarks Public

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

    Jupyter Notebook 23 3

  5. ALPINE 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 al…

    Python 7 2

Repositories

Showing 10 of 19 repositories
  • MONTE-analysis Public

    This repository contains the code and notebooks used to reproduce the analyses presented in the MONTE paper.

    ylaboratory/MONTE-analysis's past year of commit activity
    Jupyter Notebook 0 BSD-3-Clause 0 0 0 Updated Aug 28, 2026
  • MONTE Public

    MONTE:Methylation-based Observation Normalizationand Tumor purity Estimation

    ylaboratory/MONTE's past year of commit activity
    Python 0 BSD-3-Clause 1 0 0 Updated Aug 28, 2026
  • splitpea-pancancer-analysis Public
    ylaboratory/splitpea-pancancer-analysis's past year of commit activity
    Python 1 BSD-3-Clause 0 0 0 Updated Jun 24, 2026
  • splitpea-package Public

    Splitpea Python package for building rewired protein-protein interaction networks from alternative splicing events

    ylaboratory/splitpea-package's past year of commit activity
    Jupyter Notebook 2 BSD-3-Clause 0 0 0 Updated Apr 10, 2026
  • ARUNA Public

    ARUNA: Slice-based self-supervised imputation for upscaling DNA methylation sequencing assays

    ylaboratory/ARUNA's past year of commit activity
    Python 2 BSD-3-Clause 0 0 0 Updated Jan 30, 2026
  • 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 56 BSD-3-Clause 9 0 0 Updated Dec 10, 2025
  • methylation-classification Public

    Ontology-aware multi-label classification of human tissues/cells from 450K DNA methylation data

    ylaboratory/methylation-classification's past year of commit activity
    Jupyter Notebook 4 1 0 1 Updated Dec 8, 2025
  • gene-embedding-benchmarks Public

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

    ylaboratory/gene-embedding-benchmarks's past year of commit activity
    Jupyter Notebook 23 BSD-3-Clause 3 0 0 Updated Nov 29, 2025
  • ANDES Public

    A set of python scripts for comparing similiarity between genesets using gene embeddings.

    ylaboratory/ANDES's past year of commit activity
    Jupyter Notebook 5 BSD-3-Clause 3 0 0 Updated Nov 12, 2025
  • seismic-analysis Public

    Analysis and code for the Lai et al. 2025 Nature Communications paper, "Disentangling associations between complex traits and cell types with seismic"

    ylaboratory/seismic-analysis's past year of commit activity
    R 8 BSD-3-Clause 1 0 0 Updated Oct 14, 2025
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