CytofDR: CyTOF Dimension Reduction Framework

CytofDR is a framework of dimension reduction (DR) and its evaluation for both Cytometry by Time-of-Flight (CyTOF) and general-purpose usages. It allows you to conveniently run many different DRs at one place and then evaluate them to pick your embedding using our extensive evaluation framework!

Why wait? Try this example below and start your DR journey:

>>> import numpy as np
>>> from CytofDR import dr
>>> expression = np.loadtxt(fname="PATH_To_Expression_Matrix", dtype=float, skiprows=1, delimiter=",")
>>> results = dr.run_dr_methods(methods = ["UMAP", "open_tsne"])
>>> results.evaluate(category = ["global", "local", "downstream"])
>>> results.rank_dr_methods()

Getting Started

• Installation Guide
• Quickstart Guide

Tutorial

• IO and Preprocessing with PyCytoData
• DR Methods and Usage
• Choosing a DR Method
• Evaluation Metrics
• Custom DR Evaluations
• Save DR and Evaluation Results
• Optimizations: PCD and ANNOY

Development

• Contribution Guideline
• Building and Testing
• Development and Roadmap
• Changelog
• License

Full API Reference

• Full API Reference

Resources

For more resources on our labs, collaborators, and related projects, please visit the following:

• Our paper

• CytofDR Playground

• Cytomulate

• Dr. Xinlei (Shery) Wang faculty page

• Dr. Tao Wang Lab

• Database for Actionable Immunology (DBAI) for more computational immunology-related tools

• GitHub Page for project development