Uphyloplot2

Uphyloplot2 generates phylogenetic tree visualizations from inferred chromosome copy number variation (CNV) data derived from single-cell RNA-seq (scRNA-seq) and bulk RNA-seq to support analysis of tumor clonality.

Key Features:

• Implementation: Python-based script for processing inferred CNV and dendrogram inputs.
• Input data: Accepts inferred CNV data derived from scRNA-seq and bulk RNA-seq.
• CNV sources: Integrates inferred CNV outputs from inferCNV, CaSpER, and HoneyBADGER.
• Dendrogram support: Accepts Newick-formatted dendrogram files as input.
• Phylogenetic plotting: Generates phylogenetic tree plots from inferred RNA-seq CNV profiles or Newick trees.
• Biological focus: Targets analysis of tumor clonality and subclonal architecture using chromosome CNVs.

Scientific Applications:

• Tumor clonality analysis: Visualizing clonal relationships among tumor cells using CNV-inferred phylogenies.
• Subclone identification: Inferring tumor subclonal architecture from scRNA-seq or bulk RNA-seq-derived CNVs when single-cell DNA sequencing is limited.
• Cancer genomics visualization: Communicating tumor evolution and intratumoral heterogeneity through CNV-based phylogenetic plots.

Methodology:

Python-based script that accepts inferred chromosome CNV profiles from scRNA-seq or bulk RNA-seq, ingests outputs from inferCNV, CaSpER, and HoneyBADGER or Newick-formatted dendrograms, and renders phylogenetic tree plots.