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Updated: May 21, 2025

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

CytoSimplex: visualizing single-cell fates and transitions on a simplex.

Jialin Liu¹, Yichen Wang¹, Chen Li¹

¹Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, United States.

Bioinformatics (Oxford, England)

|March 22, 2025

Summary

This summary is machine-generated.

Researchers developed CytoSimplex, a novel computational approach to visualize cell differentiation trajectories. This tool quantifies cell fate commitment and potential, aiding the study of developmental processes.

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Last Updated: May 21, 2025

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A Combinatorial Single-cell Approach to Characterize the Molecular and Immunophenotypic Heterogeneity of Human Stem and Progenitor Populations

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Published on: October 25, 2018

Area of Science:

Single-cell biology
Developmental biology
Computational biology

Background:

Cell differentiation follows complex trajectories, often involving multipotent progenitors.
Single-cell transcriptomic and epigenomic data offer insights into these trajectories.
Current visualization methods like UMAP lack direct interpretability for cell differentiation.

Purpose of the Study:

To develop a novel computational approach for visualizing and quantifying cell differentiation.
To provide researchers with a tool to understand cell fate commitment and potential.
To introduce CytoSimplex, an open-source package for intuitive visualization of cell differentiation.

Main Methods:

Developed a new approach to map single cells within a simplex defined by terminally differentiated cell types.
Implemented the approach in an open-source package named CytoSimplex.
Utilized R and Python for the implementation, offering 2D ternary and 3D quaternary plots.

Main Results:

CytoSimplex quantifies and visualizes current cell fate commitment.
CytoSimplex visualizes future cell potential.
The tool provides intuitive 2D and 3D visualizations of cell differentiation.

Conclusions:

CytoSimplex offers a new method to interpret single-cell data in the context of cell differentiation.
The tool aids in understanding cell type transitions and characterizing developmental processes.
CytoSimplex is available as an open-source package in R and Python for broader research application.