umap-visualization

Interactive UMAP visualization of ALPHAGenome DNA foundation model embeddings across the human genome (hg38). Live demo via GitHub Pages.

Reproducible single-cell RNA-seq analysis of glioblastoma-associated myeloid cells from GEO dataset GSE131928 using R and Seurat. Includes clustering, UMAP visualization, marker identification, KDM6B expression analysis and figure reproduction from a published study.

fcsumap - gated multi-sample flow-cytometry UMAP A single R script that takes a folder of FCS files, applies a declarative gating strategy, and produces one shared UMAP embedding across all samples, plus the figures and tables needed to interpret and QC it.

TRIDENT is a Blender add-on that allows plotting of 3D Visualizations of UMAP, t-SNE, PCAs in a fast, reliable way.

This repo builds an interactive view that uses the ESM2 foundation model. It generates embeddings from protein sequences and visualize them in a 2D latent space. The goal is to explore whether proteins with similar biological properties cluster together naturally and to provide insights into what protein language models learn from aa sequence data

This is a University project for the Machine Learning course