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: ), Aaron Lun [aut] (ORCID: ), Charlotte Soneson [aut] (ORCID: ), Michael Stadler [aut] (ORCID: )

Maintainer: Kevin Rue-Albrecht <kevinrue67 at gmail.com>

Citation (from within R, enter 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	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

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

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)
macOS Binary (x86_64)
macOS Binary (arm64)
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