veloviz
VeloViz: RNA-velocity informed 2D embeddings for visualizing cell state trajectories
Bioconductor version: Release (3.19)
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("veloviz")
):
Installation
To install this package, start R (version "4.4") 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 | ||
NEWS | Text |
Details
biocViews | DimensionReduction, GeneExpression, RNASeq, Sequencing, Software, Transcriptomics, Visualization |
Version | 1.10.0 |
In Bioconductor since | BioC 3.14 (R-4.1) (3 years) |
License | GPL-3 |
Depends | R (>= 4.1) |
Imports | Rcpp, Matrix, igraph, mgcv, RSpectra, grDevices, graphics, stats |
System Requirements | |
URL |
See More
Suggests | knitr, rmarkdown, testthat |
Linking To | Rcpp |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | veloviz_1.10.0.tar.gz |
Windows Binary | veloviz_1.10.0.zip |
macOS Binary (x86_64) | veloviz_1.10.0.tgz |
macOS Binary (arm64) | veloviz_1.10.0.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 |