Skip to content
@ylaboratory

ylaboratory

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

Pinned Loading

  1. ETNA ETNA Public

    Embeddings to Network Alignment - align biological networks between two species

    Python 9 4

  2. flambe flambe Public

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

    Jupyter Notebook 6

  3. seismic seismic Public

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

    R 25 5

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

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

    Jupyter Notebook 18 2

  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 5 1

Repositories

Showing 10 of 17 repositories
  • ARUNA Public

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

    ylaboratory/ARUNA’s past year of commit activity
    Python 0 0 0 0 Updated Jan 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 Jan 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
    Python 1 BSD-3-Clause 0 0 0 Updated Dec 15, 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 25 BSD-3-Clause 5 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 18 BSD-3-Clause 2 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 2 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 5 BSD-3-Clause 0 0 0 Updated Oct 14, 2025
  • 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. The paper is available on Genome Research.

    ylaboratory/ALPINE’s past year of commit activity
    Python 5 BSD-3-Clause 1 0 0 Updated Sep 16, 2025
  • ALPINE-analysis Public

    This repository contains the demo and source code used in the ALPINE. If you want to learn more about the ALPINE, follow the link below.

    ylaboratory/ALPINE-analysis’s past year of commit activity
    Jupyter Notebook 1 1 0 0 Updated Sep 12, 2025
View all repositories

People

This organization has no public members. You must be a member to see who’s a part of this organization.

Top languages

Loading…

Most used topics

Loading…