velociraptor

DOI: 10.18129/B9.bioc.velociraptor  

Toolkit for Single-Cell Velocity

Bioconductor version: Release (3.16)

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] , Aaron Lun [aut] , Charlotte Soneson [aut] , Michael Stadler [aut]

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

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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")

 

HTML	R Script	User's guide
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Coverage, GeneExpression, Sequencing, SingleCell, Software
Version	1.8.0
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 years)
License	MIT + file LICENSE
Depends	SummarizedExperiment
Imports	methods, stats, Matrix, BiocGenerics, reticulate, S4Vectors, DelayedArray, basilisk, zellkonverter, scuttle, SingleCellExperiment, BiocParallel, BiocSingular
LinkingTo
Suggests	BiocStyle, testthat, knitr, rmarkdown, pkgdown, scran, scater, scRNAseq, Rtsne, graphics, grDevices, ggplot2, cowplot, GGally, patchwork, metR
SystemRequirements
Enhances
URL	https://github.com/kevinrue/velociraptor
BugReports	https://github.com/kevinrue/velociraptor/issues
Depends On Me	OSCA.advanced
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	velociraptor_1.8.0.tar.gz
Windows Binary	velociraptor_1.8.0.zip (64-bit only)
macOS Binary (x86_64)	velociraptor_1.8.0.tgz
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