CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework
Machine learning for Analysis of Proteomics in Spatial biology - Nature Communications
Code to implement the hierarchical cross-entropy loss for single-cell annotation models
Cartography of Genomic Interactions Enables Deep Analysis of Single-Cell Expression Data (Nature Communications, 2023)
singleCellNet in Python
A small GUI application for counting cells in microscope images
A single-nucleus RNA-seq reference of the 4-week rat kidney for cell type annotation and label transfer.
Advanced VAE-based pipeline for automated cell type annotation in single-cell RNA-seq data with Optuna optimization and 99%+ accuracy
Consists of scripts and workflows used for single cell annotation
Assigning cell labels w/o ref data (Tabula Sapiens)
Basic scRNA-seq analysis in Seurat using GBM data
Semi-Supervised Annotation of scRNA-seq Data
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