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Uphyloplot2: visualizing phylogenetic trees from single-cell RNA-seq data
BACKGROUND: Recent advances in single cell sequencing technologies allow for greater resolution in assessing tumor clonality using chromosome copy number variations (CNVs). While single cell DNA sequencing technologies are ideal to identify tumor sub-clones, they remain expensive and in contrast to...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8180062/ https://www.ncbi.nlm.nih.gov/pubmed/34090344 http://dx.doi.org/10.1186/s12864-021-07739-3 |
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author | Kurtenbach, Stefan Cruz, Anthony M. Rodriguez, Daniel A. Durante, Michael A. Harbour, J. William |
author_facet | Kurtenbach, Stefan Cruz, Anthony M. Rodriguez, Daniel A. Durante, Michael A. Harbour, J. William |
author_sort | Kurtenbach, Stefan |
collection | PubMed |
description | BACKGROUND: Recent advances in single cell sequencing technologies allow for greater resolution in assessing tumor clonality using chromosome copy number variations (CNVs). While single cell DNA sequencing technologies are ideal to identify tumor sub-clones, they remain expensive and in contrast to single cell RNA-seq (scRNA-seq) methods are more limited in the data they generate. However, CNV data can be inferred from scRNA-seq and bulk RNA-seq, for which several tools have been developed, including inferCNV, CaSpER, and HoneyBADGER. Inferences regarding tumor clonality from CNV data (and other sources) are frequently visualized using phylogenetic plots, which previously required time-consuming and error-prone, manual analysis. RESULTS: Here, we present Uphyloplot2, a python script that generates phylogenetic plots directly from inferred RNA-seq data, or any Newick formatted dendrogram file. The tool is publicly available at https://github.com/harbourlab/UPhyloplot2/. CONCLUSIONS: Uphyloplot2 is an easy-to-use tool to generate phylogenetic plots to depict tumor clonality from scRNA-seq data and other sources. |
format | Online Article Text |
id | pubmed-8180062 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-81800622021-06-07 Uphyloplot2: visualizing phylogenetic trees from single-cell RNA-seq data Kurtenbach, Stefan Cruz, Anthony M. Rodriguez, Daniel A. Durante, Michael A. Harbour, J. William BMC Genomics Software BACKGROUND: Recent advances in single cell sequencing technologies allow for greater resolution in assessing tumor clonality using chromosome copy number variations (CNVs). While single cell DNA sequencing technologies are ideal to identify tumor sub-clones, they remain expensive and in contrast to single cell RNA-seq (scRNA-seq) methods are more limited in the data they generate. However, CNV data can be inferred from scRNA-seq and bulk RNA-seq, for which several tools have been developed, including inferCNV, CaSpER, and HoneyBADGER. Inferences regarding tumor clonality from CNV data (and other sources) are frequently visualized using phylogenetic plots, which previously required time-consuming and error-prone, manual analysis. RESULTS: Here, we present Uphyloplot2, a python script that generates phylogenetic plots directly from inferred RNA-seq data, or any Newick formatted dendrogram file. The tool is publicly available at https://github.com/harbourlab/UPhyloplot2/. CONCLUSIONS: Uphyloplot2 is an easy-to-use tool to generate phylogenetic plots to depict tumor clonality from scRNA-seq data and other sources. BioMed Central 2021-06-05 /pmc/articles/PMC8180062/ /pubmed/34090344 http://dx.doi.org/10.1186/s12864-021-07739-3 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Software Kurtenbach, Stefan Cruz, Anthony M. Rodriguez, Daniel A. Durante, Michael A. Harbour, J. William Uphyloplot2: visualizing phylogenetic trees from single-cell RNA-seq data |
title | Uphyloplot2: visualizing phylogenetic trees from single-cell RNA-seq data |
title_full | Uphyloplot2: visualizing phylogenetic trees from single-cell RNA-seq data |
title_fullStr | Uphyloplot2: visualizing phylogenetic trees from single-cell RNA-seq data |
title_full_unstemmed | Uphyloplot2: visualizing phylogenetic trees from single-cell RNA-seq data |
title_short | Uphyloplot2: visualizing phylogenetic trees from single-cell RNA-seq data |
title_sort | uphyloplot2: visualizing phylogenetic trees from single-cell rna-seq data |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8180062/ https://www.ncbi.nlm.nih.gov/pubmed/34090344 http://dx.doi.org/10.1186/s12864-021-07739-3 |
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