velociraptor
This is the development version of velociraptor; for the stable release version, see velociraptor.
Toolkit for Single-Cell Velocity
Bioconductor version: Development (3.21)
This package provides Bioconductor-friendly wrappers for RNA velocity calculations in single-cell RNA-seq data. We use the basilisk package to manage Conda environments, and the zellkonverter package to convert data structures between SingleCellExperiment (R) and AnnData (Python). The information produced by the velocity methods is stored in the various components of the SingleCellExperiment class.
Author: Kevin Rue-Albrecht [aut, cre] (ORCID:
Maintainer: Kevin Rue-Albrecht <kevinrue67 at gmail.com>
citation("velociraptor")):
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("velociraptor")
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("velociraptor")| User's guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Coverage, GeneExpression, Sequencing, SingleCell, Software |
| Version | 1.17.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (4 years) |
| License | MIT + file LICENSE |
| Depends | SummarizedExperiment |
| Imports | methods, stats, Matrix, BiocGenerics, reticulate, S4Vectors, DelayedArray, basilisk, zellkonverter, scuttle, SingleCellExperiment, BiocParallel, BiocSingular |
| System Requirements | |
| URL | https://github.com/kevinrue/velociraptor |
| Bug Reports | https://github.com/kevinrue/velociraptor/issues |
See More
| Suggests | BiocStyle, testthat, knitr, rmarkdown, pkgdown, scran, scater, scRNAseq, Rtsne, graphics, grDevices, ggplot2, cowplot, GGally, patchwork, metR |
| Linking To | |
| 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 | velociraptor_1.17.0.tar.gz |
| Windows Binary (x86_64) | velociraptor_1.17.0.zip (64-bit only) |
| macOS Binary (x86_64) | velociraptor_1.17.0.tgz |
| macOS Binary (arm64) | velociraptor_1.17.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/velociraptor |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/velociraptor |
| Bioc Package Browser | https://code.bioconductor.org/browse/velociraptor/ |
| Package Short Url | https://bioconductor.org/packages/velociraptor/ |
| Package Downloads Report | Download Stats |