scvi

A PKHeX compatible dumper and injector for Pokémon Scarlet and Violet.

Regularized scVI for complex multiome single-cell/nucleus datasets: ambient RNA correction, dispersion prior, and batch-free decoder act as structural inductive biases that make large-architecture VAEs well-behaved without per-dataset tuning.

A PKX encryptor and decryptor

Benchmarking AE, VAE, and scVI autoencoders to predict optimal latent dimension from cell-type complexity (K) in single-cell RNA-seq, using a trust-aware evidence framework across 5 curated datasets from PBMC to atlas-scale.

Single-cell RNA-seq analysis of the Salcher 2022 LuCA lung cancer atlas — scanpy + scVI + LightGBM, leave-one-study-out CV

A stem-cell differentiation copilot for computational biology teams — CABS 2026 intern project.

Four-phase scRNA-seq pipeline characterizing Tbx1 conditional knockout in cardiopharyngeal progenitors. Nextflow DSL2 + Seurat + scVI + DESeq2 + clusterProfiler.

Lightweight, GPU-accelerated single-cell RNA-seq workflow for exploring the colorectal tumor microenvironment (CRC-TME) using Scanpy and scVI.

Single-cell RNA-seq and TCR repertoire analysis workflows for paediatric immune ageing using Scanpy, scVI, Milo and Dandelion.

Public portfolio of reproducible bioinformatics and computational biology workflows developed for RNA-seq, single-cell analysis, ageing biology and systems biology projects. It includes my main immune-aging workflow. Selected subprojects include modular Snakemake pipelines, QC/reporting outputs and documented analysis workflows.

Reproducible scRNA-seq reference projection pipeline for TIL cell type annotation, benchmarking CCA vs scVI/scANVI for immunotherapy-oriented analysis.