RT Journal Article
SR Electronic
T1 SPRING: a kinetic interface for visualizing high dimensional single-cell expression data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 090332
DO 10.1101/090332
A1 Caleb Weinreb
A1 Samuel Wolock
A1 Allon Klein
YR 2016
UL http://biorxiv.org/content/early/2016/11/29/090332.abstract
AB Motivation Single-cell gene expression profiling technologies can map the cell states in a tissue or organism. As these technologies become more common, there is a need for computational tools to explore the data they produce. In particular, existing data visualization approaches are imperfect for studying continuous gene expression topologies.Results Force-directed layouts of k-nearest-neighbor graphs can visualize continuous gene expression topologies in a manner that preserves high-dimensional relationships and allows manually exploration of different stable two-dimensional representations of the same data. We implemented an interactive web-tool to visualize single-cell data using force-directed graph layouts, called SPRING. SPRING reveals more detailed biological relationships than existing approaches when applied to branching gene expression trajectories from hematopoietic progenitor cells. Visualizations from SPRING are also more reproducible than those of stochastic visualization methods such as tSNE, a state-of-the-art tool.Availability https://kleintools.hms.harvard.edu/tools/spring.html, https://github.com/AllonKleinLab/SPRING/Contact calebsw{at}gmail.com, allon.klein{at}hms.harvard.edu