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velociraptor

Toolkit for Single-Cell Velocity

Bioconductor version: Release (3.17)

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>

Citation (from within R, enter citation("velociraptor")):

Installation

To install this package, start R (version "4.3") 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")
User's guide HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Coverage, GeneExpression, Sequencing, SingleCell, Software
Version 1.10.0
In Bioconductor since BioC 3.12 (R-4.0) (3 years)
License MIT + file LICENSE
Depends SummarizedExperiment
Imports methods, stats, Matrix, BiocGenerics, reticulate, S4Vectors, DelayedArray, basilisk, zellkonverter, scuttle, SingleCellExperiment, BiocParallel, BiocSingular
Linking To
Suggests BiocStyle, testthat, knitr, rmarkdown, pkgdown, scran, scater, scRNAseq, Rtsne, graphics, grDevices, ggplot2, cowplot, GGally, patchwork, metR
System Requirements
Enhances
URL https://github.com/kevinrue/velociraptor
Bug Reports https://github.com/kevinrue/velociraptor/issues
See More
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_1.10.0.tar.gz
Windows Binary velociraptor_1.10.0.zip
macOS Binary (x86_64) velociraptor_1.10.0.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