ylaboratory

All

17 repositories

splitpea-package
Public
Splitpea Python package for building rewired protein-protein interaction networks from alternative splicing events
bioinformatics protein-protein-interaction ppi-networks
bioinformatics protein-protein-interaction ppi-networks computional-biology
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•0•1•0•0•Updated Feb 12, 2026Feb 12, 2026
MONTE
Public
MONTE:Methylation-based Observation Normalizationand Tumor purity Estimation
machine-learning cancer methylation
machine-learning cancer methylation bayesian methylation-microarrays ols-regression epigenomics
Python
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BSD 3-Clause "New" or "Revised" License
•1•0•0•0•Updated Feb 4, 2026Feb 4, 2026
ARUNA
Public
ARUNA: Slice-based self-supervised imputation for upscaling DNA methylation sequencing assays
Python
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BSD 3-Clause "New" or "Revised" License
•0•1•0•0•Updated Jan 30, 2026Jan 30, 2026
seismic
Public
Seismic R package. Discover cell type-trait associations in minutes for GWAS and single-cell RNA-sequencing data
gwas single-cell scrna
gwas single-cell scrna
R
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BSD 3-Clause "New" or "Revised" License
•6•27•0•0•Updated Dec 10, 2025Dec 10, 2025
methylation-classification
Public
Ontology-aware multi-label classification of human tissues/cells from 450K DNA methylation data
bioinformatics dna-methylation multi-label-classification
bioinformatics dna-methylation multi-label-classification tissue-classification
Jupyter Notebook
•1•4•0•1•Updated Dec 8, 2025Dec 8, 2025
gene-embedding-benchmarks
Public
Benchmarking gene embeddings on single, paired, and gene set tasks
benchmarking gene-embedding
benchmarking gene-embedding
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•2•18•0•0•Updated Nov 29, 2025Nov 29, 2025
ANDES
Public
A set of python scripts for comparing similiarity between genesets using gene embeddings.
geneset-enrichment gsea gene-embedding
geneset-enrichment gsea gene-embedding geneset-enrichment-analysis gene-embeddings
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•3•2•0•0•Updated Nov 12, 2025Nov 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"
gwas scrna-seq scrna-seq-analysis
gwas scrna-seq scrna-seq-analysis
R
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BSD 3-Clause "New" or "Revised" License
•1•6•0•0•Updated Oct 14, 2025Oct 14, 2025
ALPINE
Public
ALPINE is a semi-supervised non-negative matrix factorization (NMF) framework designed to effectively distinguish between multiple phenotypic conditions based o…
scrna-seq batch-effects non-negative-matrix-factorization
scrna-seq batch-effects non-negative-matrix-factorization bioinformatics-tool
Python
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BSD 3-Clause "New" or "Revised" License
•2•5•0•0•Updated Sep 16, 2025Sep 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.
scrna-seq batch-effects non-negative-matrix-factorization
scrna-seq batch-effects non-negative-matrix-factorization bioinformatics-tool
Jupyter Notebook
•1•1•0•0•Updated Sep 12, 2025Sep 12, 2025
flambe
Public
datasets for tissue and tool named entity recognition, annotation files for biological workflow extraction, and disambiguation files
natural-language-processing bioinformatics named-entity-recognition
natural-language-processing bioinformatics named-entity-recognition single-cell bionlp multiverse-analysis
Jupyter Notebook
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Creative Commons Attribution 4.0 International
•1•6•0•0•Updated Jul 8, 2024Jul 8, 2024
biomedical
Public
Tools for curating biomedical training data for large-scale language modeling
Python
•119•1•0•0•Updated Jun 4, 2024Jun 4, 2024
ar-biorxiv-style
Public
A Latex style and template for paper preprints (based on NIPS style)
TeX
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MIT License
•368•0•0•0•Updated Mar 12, 2024Mar 12, 2024
splitpea
Public
A tool for calculating PPI network rewiring due to alternative splicing
bioinformatics cancer protein-protein-interaction
bioinformatics cancer protein-protein-interaction ppi-networks splicing
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•1•1•0•0•Updated Jan 15, 2024Jan 15, 2024
ETNA
Public
Embeddings to Network Alignment - align biological networks between two species
computational-biology network-alignment bioinformatics-tool
computational-biology network-alignment bioinformatics-tool ppi-networks protein-protein-interaction-network
Python
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BSD 3-Clause "New" or "Revised" License
•5•9•0•1•Updated Sep 8, 2023Sep 8, 2023
kraken2
Public
The second version of the Kraken taxonomic sequence classification system
C++
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MIT License
•300•0•0•0•Updated Jun 1, 2021Jun 1, 2021
krakenuniq
Public
🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
C++
•42•0•0•0•Updated May 27, 2021May 27, 2021