Package: velociraptor 1.23.0

Kevin Rue-Albrecht

velociraptor: Toolkit for Single-Cell Velocity

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.

Authors:Kevin Rue-Albrecht [aut, cre], Aaron Lun [aut], Charlotte Soneson [aut], Michael Stadler [aut]

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manual.pdf |manual.html✨
card.svg |card.png
velociraptor/json (API)
NEWS

# Install 'velociraptor' in R:
install.packages('velociraptor', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/kevinrue/velociraptor/issues

On BioConductor:velociraptor-1.23.0(bioc 3.24)velociraptor-1.22.0(bioc 3.23)

singlecellgeneexpressionsequencingcoveragerna-velocity

7.83 score 61 stars 62 scripts 416 downloads 6 exports 49 dependencies

Last updated from:280d0504ed. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE243
linux-devel-x86_64WARNING1331
source / vignettesOK1256
linux-release-x86_64WARNING1233
macos-release-arm64WARNING782
macos-oldrel-arm64WARNING578
windows-develWARNING1744
windows-releaseWARNING1629
windows-oldrelWARNING1588
wasm-releaseOK224

Exports:.grid_vectorsembedVelocitygridVectorsplotVelocityplotVelocityStreamscvelo

Dependencies:abindassortheadbasiliskbeachmatBHBiobaseBiocGenericsBiocParallelBiocSingularclicodetoolscpp11DelayedArraydir.expiryfilelockformatRfutile.loggerfutile.optionsgenericsGenomicRangeshereIRangesirlbajsonlitelambda.rlatticeMatrixMatrixGenericsmatrixStatspngrappdirsRcppRcppTOMLreticulaterlangrprojrootrsvdS4ArraysS4VectorsScaledMatrixscuttleSeqinfoSingleCellExperimentsnowSparseArraySummarizedExperimentwithrXVectorzellkonverter

Computing RNA velocity in a Bioconductor framework

Kevin Rue-Albrecht, Aaron Lun, Charlotte Soneson

Rendered fromvelociraptor.Rmdusingknitr::rmarkdownon May 24 2026.

Last update: 2024-05-30
Started: 2021-02-22

Readme and manuals

Help Manual

Help pageTopics
Project velocities onto an embeddingembedVelocity embedVelocity,ANY-method embedVelocity,SingleCellExperiment-method
Summarize vectors into a gridgridVectors gridVectors,ANY-method gridVectors,SingleCellExperiment-method
Phase and velocity graphs for a set of genesplotVelocity
Velocity stream plot in low-dimensional spaceplotVelocityStream
RNA velocity with 'scVelo'scvelo scvelo,ANY-method scvelo,SingleCellExperiment-method scvelo,SummarizedExperiment-method