DOI: 10.18129/B9.bioc.veloviz  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see veloviz.

VeloViz: RNA-velocity informed 2D embeddings for visualizing cell state trajectories

Bioconductor version: 3.16

VeloViz uses each cell’s current observed and predicted future transcriptional states inferred from RNA velocity analysis to build a nearest neighbor graph between cells in the population. Edges are then pruned based on a cosine correlation threshold and/or a distance threshold and the resulting graph is visualized using a force-directed graph layout algorithm. VeloViz can help ensure that relationships between cell states are reflected in the 2D embedding, allowing for more reliable representation of underlying cellular trajectories.

Author: Lyla Atta [aut, cre] , Jean Fan [aut] , Arpan Sahoo [aut]

Maintainer: Lyla Atta <lylaatta at>

Citation (from within R, enter citation("veloviz")):


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HTML R Script Visualizing cell cycle trajectory in MERFISH data using VeloViz
PDF   Reference Manual
Text   NEWS


biocViews DimensionReduction, GeneExpression, RNASeq, Sequencing, Software, Transcriptomics, Visualization
Version 1.4.0
In Bioconductor since BioC 3.14 (R-4.1) (1.5 years)
License GPL-3
Depends R (>= 4.1)
Imports Rcpp, Matrix, igraph, mgcv, RSpectra, grDevices, graphics, stats
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Suggests knitr, rmarkdown, testthat
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