#40 · Tools & infrastructure

Browser and agent-driven tools standardize EV, transcriptomic and omics plotting workflows

The common thread across these items is software that makes standardized omics or biophysical measurements interrogable through processing and visualization. PHoNUPS is open-source R software that standardizes processing, statistics, and histogram/contour visualization of extracellular vesicle size and zeta potential across multiple instruments. PPGLomics is a web platform integrating TCGA-PCPG (n=160) and A5 SDHB (n=91) pheochromocytoma and paraganglioma transcriptomics. PlotGDP is an LLM-based agent web server that converts natural-language commands into bioinformatics plots by running curated template scripts on a remote server. What is new is access mediated by browsers or natural-language agents layered over curated, standardized inputs. ME-seq differs in kind: it is a trimodal single-nucleus profiling method reporting DNA methylation, gene expression and chromatin accessibility in aging and Alzheimer's disease mouse models, contributing data rather than tooling.