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veloviz

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


Bioconductor version: Release (3.18)

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 jhmi.edu>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("veloviz")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("veloviz")
Visualizing cell cycle trajectory in MERFISH data using VeloViz HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DimensionReduction, GeneExpression, RNASeq, Sequencing, Software, Transcriptomics, Visualization
Version 1.8.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License GPL-3
Depends R (>= 4.1)
Imports Rcpp, Matrix, igraph, mgcv, RSpectra, grDevices, graphics, stats
System Requirements
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Suggests knitr, rmarkdown, testthat
Linking To Rcpp
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package veloviz_1.8.0.tar.gz
Windows Binary veloviz_1.8.0.zip
macOS Binary (x86_64) veloviz_1.8.0.tgz
macOS Binary (arm64) veloviz_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/veloviz
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/veloviz
Bioc Package Browser https://code.bioconductor.org/browse/veloviz/
Package Short Url https://bioconductor.org/packages/veloviz/
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