RT Journal Article SR Electronic T1 PhyloVision: Interactive Software for Integrated Analysis of Single-Cell Transcriptomic and Phylogenetic Data JF bioRxiv FD Cold Spring Harbor Laboratory SP 2021.09.13.460142 DO 10.1101/2021.09.13.460142 A1 Matthew G. Jones A1 Yanay Rosen A1 Nir Yosef YR 2021 UL http://biorxiv.org/content/early/2021/09/13/2021.09.13.460142.abstract AB 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.Competing Interest StatementThe authors have declared no competing interest.