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Related Experiment Video

Updated: Nov 3, 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

Uphyloplot2: visualizing phylogenetic trees from single-cell RNA-seq data.

Stefan Kurtenbach¹, Anthony M Cruz², Daniel A Rodriguez²

¹Sylvester Comprehensive Cancer Center, Interdisciplinary Stem Cell Institute, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA. Stefan.Kurtenbach@med.miami.edu.

|June 6, 2021

Summary

This summary is machine-generated.

Uphyloplot2 simplifies tumor clonal analysis by generating phylogenetic plots directly from inferred RNA-seq data. This python script automates visualization, improving the study of tumor evolution from single-cell RNA sequencing (scRNA-seq) data.

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Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

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Published on: January 10, 2019

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

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Published on: October 16, 2018

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Area of Science:

Genomics
Computational Biology
Cancer Research

Background:

Single-cell sequencing advances tumor clonality assessment via copy number variations (CNVs).
CNV data can be inferred from single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq.
Existing tools for CNV inference include inferCNV, CaSpER, and HoneyBADGER.

Purpose of the Study:

To present Uphyloplot2, a novel python script for generating phylogenetic plots.
To enable direct visualization of tumor clonality from inferred RNA-seq data.

Main Methods:

Developed a python script, Uphyloplot2.
The script accepts inferred RNA-seq data or Newick formatted dendrogram files.
Uphyloplot2 automates the generation of phylogenetic plots.

Main Results:

Uphyloplot2 successfully generates phylogenetic plots directly from inferred RNA-seq data.
The tool provides a streamlined method for visualizing tumor clonality.
The script is publicly available on GitHub.

Conclusions:

Uphyloplot2 is an accessible tool for creating phylogenetic plots.
It facilitates the depiction of tumor clonality from scRNA-seq and other data sources.
This enhances the analysis of tumor evolution and subclonal architecture.