Overview | Downsampling for demonstration | Basic workflow | Advanced options | Session information | References
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:
velociraptor_1.23.0.tar.gz
velociraptor_1.23.0.zip(r-4.7)velociraptor_1.23.0.zip(r-4.6)velociraptor_1.23.0.zip(r-4.5)
velociraptor_1.23.0.tgz(r-4.6-any)velociraptor_1.23.0.tgz(r-4.5-any)
velociraptor_1.23.0.tar.gz(r-4.7-any)velociraptor_1.23.0.tar.gz(r-4.6-any)
velociraptor_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
velociraptor/json (API)
| # 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
Last updated from:280d0504ed. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 258 | ||
| linux-devel-x86_64 | WARNING | 1360 | ||
| source / vignettes | OK | 1271 | ||
| linux-release-x86_64 | WARNING | 1312 | ||
| macos-release-arm64 | WARNING | 796 | ||
| macos-oldrel-arm64 | WARNING | 785 | ||
| windows-devel | WARNING | 1571 | ||
| windows-release | WARNING | 1621 | ||
| windows-oldrel | WARNING | 1547 | ||
| wasm-release | OK | 263 |
Exports:.grid_vectorsembedVelocitygridVectorsplotVelocityplotVelocityStreamscvelo
Dependencies:abindassortheadbasiliskbeachmatBHBiobaseBiocGenericsBiocParallelBiocSingularclicodetoolscpp11DelayedArraydir.expiryfilelockformatRfutile.loggerfutile.optionsgenericsGenomicRangeshereIRangesirlbajsonlitelambda.rlatticeMatrixMatrixGenericsmatrixStatspngrappdirsRcppRcppTOMLreticulaterlangrprojrootrsvdS4ArraysS4VectorsScaledMatrixscuttleSeqinfoSingleCellExperimentsnowSparseArraySummarizedExperimentwithrXVectorzellkonverter
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Project velocities onto an embedding | embedVelocity embedVelocity,ANY-method embedVelocity,SingleCellExperiment-method |
| Summarize vectors into a grid | gridVectors gridVectors,ANY-method gridVectors,SingleCellExperiment-method |
| Phase and velocity graphs for a set of genes | plotVelocity |
| Velocity stream plot in low-dimensional space | plotVelocityStream |
| RNA velocity with 'scVelo' | scvelo scvelo,ANY-method scvelo,SingleCellExperiment-method scvelo,SummarizedExperiment-method |
