Package: scVeloR 0.1.0

scVeloR: RNA Velocity Analysis in R

A comprehensive R implementation of RNA velocity analysis based on the scvelo Python package. This package enables estimation of RNA velocities for single-cell RNA-seq data, supporting deterministic (steady-state), stochastic, and dynamical models. The dynamical model uses an Expectation-Maximization algorithm to infer full transcriptional kinetics including transcription, splicing, and degradation rates. The package integrates seamlessly with Seurat objects and provides visualization functions for velocity embedding, stream plots, and phase portraits.

Authors:Zaoqu Liu [aut, cre], scVelo Team [ctb]

scVeloR_0.1.0.tar.gz
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scVeloR_0.1.0.tgz(r-4.6-x86_64)scVeloR_0.1.0.tgz(r-4.6-arm64)scVeloR_0.1.0.tgz(r-4.5-x86_64)scVeloR_0.1.0.tgz(r-4.5-arm64)
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scVeloR_0.1.0.tgz(r-4.6-emscripten)
 |manual.html✨
card.svg |card.png
scVeloR/json (API)

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

Bug tracker:https://github.com/zaoqu-liu/scvelor/issues

Pkgdown/docs site:https://zaoqu-liu.github.io

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

openblascpp

3.48 score 1 stars 8 scripts 57 exports 5 dependencies

Last updated from:319e312f72 (on main). Checks:9 ERROR, 3 FAIL, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64ERROR199
linux-devel-x86_64ERROR217
source / vignettesERROR272
linux-release-arm64ERROR217
linux-release-x86_64ERROR201
macos-release-arm64ERROR134
macos-release-x86_64ERROR289
macos-oldrel-arm64FAIL78
macos-oldrel-x86_64FAIL152
windows-develERROR225
windows-releaseERROR177
windows-oldrelFAIL202
wasm-releaseOK163

Exports:assign_tauBaseDynamicscompute_divergencecompute_neighborscompute_shared_timecompute_transition_matrixcompute_velocity_from_paramscreate_velocity_seuratcross_momentsDynamicsRecoveryexport_to_anndataexport_velocity_resultsfilter_cellsfilter_genesget_connectivitiesget_embeddingget_layer_matrixget_velocity_dataimport_from_anndataimport_velocity_datalatent_timemomentsmRNAnormalize_layersplot_phaseplot_velocityplot_velocity_gridplot_velocity_streamprepare_velocityrank_velocity_genesrecover_dynamicsrecover_dynamics_multiroot_timerun_velocitysecond_order_momentsSecondOrderSteadyStateModelsplicedSplicingDynamicssteady_statetau_invtau_inv_uterminal_statesunsplicedvectorizevelocityvelocity_cell_cyclevelocity_coherencevelocity_confidencevelocity_embeddingvelocity_from_dynamicsvelocity_graphvelocity_gridvelocity_pseudotimevelocity_steady_statevelocity_stochasticvelocity_streamlinesvelocity_summary

Dependencies:latticeMatrixR6RcppRcppArmadillo

Dynamical Model Deep Dive

Zaoqu Liu

Rendered fromdynamical-model.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2026-01-25
Started: 2026-01-25

Mathematical Framework of RNA Velocity

Zaoqu Liu

Rendered fromalgorithm-theory.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2026-01-25
Started: 2026-01-25

Performance Optimization Guide

Zaoqu Liu

Rendered fromperformance-guide.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2026-01-25
Started: 2026-01-25

scVeloR: RNA Velocity Analysis in R

Zaoqu Liu

Rendered fromscVeloR-tutorial.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2026-01-25
Started: 2026-01-25

Velocity Model Comparison

Zaoqu Liu

Rendered frommodel-comparison.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2026-01-25
Started: 2026-01-25

Visualization Gallery

Zaoqu Liu

Rendered fromvisualization-gallery.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2026-01-25
Started: 2026-01-25