veloviz
This is the development version of veloviz; for the stable release version, see veloviz.
VeloViz: RNA-velocity informed 2D embeddings for visualizing cell state trajectories
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Lyla Atta <lylaatta at jhmi.edu>
citation("veloviz")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | 1.13.0 |
| 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_1.13.0.tar.gz |
| Windows Binary (x86_64) | veloviz_1.13.0.zip |
| macOS Binary (x86_64) | veloviz_1.13.0.tgz |
| macOS Binary (arm64) | veloviz_1.13.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/veloviz |
| Source Repository (Developer Access) | git clone [email protected]:packages/veloviz |
| Bioc Package Browser | https://code.bioconductor.org/browse/veloviz/ |
| Package Short Url | https://bioconductor.org/packages/veloviz/ |
| Package Downloads Report | Download Stats |