veloviz
This is the released version of veloviz; for the devel version, see veloviz.
VeloViz: RNA-velocity informed 2D embeddings for visualizing cell state trajectories
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.18.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (5 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_1.18.0.tar.gz |
| Windows Binary (x86_64) | veloviz_1.18.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | veloviz_1.18.0.tgz |
| macOS Binary (sonoma-arm64) | veloviz_1.18.0.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 |