A small library for automatical adjustment of text position in matplotlib plots to minimize overlaps.

Reference mapping for single-cell genomics

MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.

Single cell trajectory detection

Mapping out the coarse-grained connectivity structures of complex manifolds.

Single cell RNA sequencing analysis course

Fast Wilcoxon and auROC

A Bayesian model for compositional single-cell data analysis

Python module for plotting Venn diagrams of 2..6 sets

Detect doublets in single-cell RNA-seq data

Code used to benchmark Xenium

Representation Learning for detection of phenotype-associated cell subsets

Large language modeling applied to T-cell receptor (TCR) sequences.

Functional Associations using Variational Autoencoders

TCRGP, a novel Gaussian process method that can predict if TCRs recognize certain epitopes. This method can utilize different CDR sequences from both TCRα and TCRβ chains from single-cell data and …

Statistical quality evaluation of dimensionality reduction algorithms

tools in python and R for analyzing biological count data, especially from single cell RNAseq

Wishbone is an algorithm to align cells along developmental trajectories with branches

Single cell pipelines

Cell line HLA types and neoepitope catalog from TCLP

This is the repository for the code used in my dissertation, for tidied code, please view https://github.com/RcwYuen/TCR-Embeddings

Code used to benchmark Xenium

Repository containing all the scripts and the models used for the analysis