veloviz

DOI: 10.18129/B9.bioc.veloviz  

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

Bioconductor version: Release (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 jhmi.edu>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

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
LinkingTo	Rcpp
Suggests	knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

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

Source Package	veloviz_1.4.0.tar.gz
Windows Binary	veloviz_1.4.0.zip
macOS Binary (x86_64)	veloviz_1.4.0.tgz
macOS Binary (arm64)	veloviz_1.4.0.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/
Package Downloads Report	Download Stats