veloviz

DOI: 10.18129/B9.bioc.veloviz    

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

Bioconductor version: Release (3.14)

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 "4.1") and enter:

if (!requireNamespace("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 1.0.0
In Bioconductor since BioC 3.14 (R-4.1) (< 6 months)
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
Links To Me
Build Report  

Package Archives

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

Source Package veloviz_1.0.0.tar.gz
Windows Binary veloviz_1.0.0.zip
macOS 10.13 (High Sierra) veloviz_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/veloviz
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/veloviz
Package Short Url https://bioconductor.org/packages/veloviz/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.14 Source Archive

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