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Bioconductor - velociraptor

velociraptor

This is the released version of velociraptor; for the devel version, see velociraptor.

Toolkit for Single-Cell Velocity

Bioconductor version: Release (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: 0000-0003-3899-3872 , Aaron Lun [aut] ORCID: 0000-0002-3564-4813 , Charlotte Soneson [aut] ORCID: 0000-0003-3833-2169 , Michael Stadler [aut] ORCID: 0000-0002-2269-4934

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")

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")
Details biocViews Coverage, GeneExpression, Sequencing, SingleCell, Software Version 1.18.0 In Bioconductor since BioC 3.12 (R-4.0) (4.5 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 OSCA.advanced Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

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

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