High-throughput data collection technologies are becoming increasingly common in many fields, especially in biomedical applications involving single cell data genomics and transcriptomics. These introduce a rising need for exploratory analysis to reveal and understand hidden structure in the collected (high-dimensional) Big Data. A crucial aspect in such analysis is the separation of intrinsic data geometry from data distribution, as (a) the latter is typically biased by collection artifacts and data availability, and (b) rare subpopulations and sparse transitions between meta-stable states are often of great interest in biomedical data analysis. In this talk, I will show several tools that leverage manifold learning, graph signal processing, and harmonic analysis for biomedical (in particular, genomic/proteomic) data exploration, with emphasis on visualization, nonlinear feature extraction, and multiresolution analysis. A common thread in the presented tools is the construction of a data-driven diffusion geometry that both captures intrinsic structure in data and provides a generalization of Fourier harmonics on it. These, in turn, are used to process data features along the data geometry for multiple purposes, including preprocessing of single cell data and enabling batch-level geometric exploration, e.g., over and between medical conditions, health states, and drug reactions.