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bioRxiv · 10.1101/2021.09.13.460142

PhyloVision: Interactive Software for Integrated Analysis of Single-Cell Transcriptomic and PhylogeneticData

Jones, M. G.·Rosen, Y.·Yosef, N.
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Abstract

Recent advances in CRISPR-Cas9 engineering and single-cell assays have enabled the simultaneous measurement of single-cell transcriptomic and phylogenetic profiles. However, there are few computational tools enabling users to integrate and derive insight from a joint analysis of these two modalities. Here, we describe PhyloVision: an open source software for interactively exploring data from both modalities and for identifying and interpreting heritable gene modules whose concerted expression are associated with phylogenetic relationships. PhyloVision provides a feature-rich, interactive, and shareable web-based report for investigating these modules, while also supporting several other data and meta-data exploration capabilities. We demonstrate the utility of PhyloVision using a published dataset of metastatic lung adenocarcinoma cells, whose phylogeny was resolved using a CRISPR/Cas9-based lineage-tracing system. Together, we anticipate that PhyloVision and the methods it implements will be a useful resource for scalable and intuitive data exploration for any assay that simultaneously measures cell state and lineage.

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Jones, M. G., Rosen, Y., Yosef, N.. 2021-09-13. PhyloVision: Interactive Software for Integrated Analysis of Single-Cell Transcriptomic and PhylogeneticData. https://doi.org/10.1101/2021.09.13.460142

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