Welcome to Omicverse✨’s documentation!¶

OmicVerse v2 is a unified Python project for modern transcriptomics and multi-omics analysis. It brings together bulk RNA-seq, single-cell, spatial transcriptomics, downstream visualization, model-based analysis, and AI-assisted workflows in one package and documentation system.

To get started with omicverse, check out the Installation and Tutorials.

To get started with OmicClaw, check out the OmicClaw Gateway Tutorials

Documentation Tracks¶

• Installation: environment setup, PyTorch, conda, pip, and Docker.
• Tutorial Overview: the full markdown map of the tutorial structure in mkdocs.yml.
• Bulk Tutorials: bulk RNA-seq preprocessing, DE, WGCNA, and deconvolution.
• Single-Cell Tutorials: preprocessing, annotation, trajectory, metacells, and multi-omics.
• Spatial Tutorials: spatial preprocessing, deconvolution, and downstream analysis.
• Foundation Model and AI Tutorials: ov.fm, OmicClaw / gateway deployment, coding workflows, and MCP.
• Plotting Tutorials: single-cell, bulk, palette, and color-system visualization.

For more details about the omicverse framework, please check out our publication.