Package: veloviz 1.13.0

Lyla Atta

veloviz: VeloViz: RNA-velocity informed 2D embeddings for visualizing cell state trajectories

VeloViz uses each cell’s current observed and predicted future transcriptional states inferred from RNA velocity analysis to build a nearest neighbor graph between cells in the population. Edges are then pruned based on a cosine correlation threshold and/or a distance threshold and the resulting graph is visualized using a force-directed graph layout algorithm. VeloViz can help ensure that relationships between cell states are reflected in the 2D embedding, allowing for more reliable representation of underlying cellular trajectories.

Authors:Lyla Atta [aut, cre], Jean Fan [aut], Arpan Sahoo [aut]

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veloviz.pdf |veloviz.html✨
veloviz/json (API)
NEWS

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

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • pancreas - Pancreas scRNA-seq data
  • vel - MERFISH velocity subset

On BioConductor:veloviz-1.13.0(bioc 3.21)veloviz-1.12.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

transcriptomicsvisualizationgeneexpressionsequencingrnaseqdimensionreduction

4.00 score 6 scripts 132 downloads 9 exports 16 dependencies

Last updated 23 days agofrom:53cb575e70. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-win-x86_64OKOct 31 2024
R-4.5-linux-x86_64OKOct 31 2024
R-4.4-win-x86_64OKOct 31 2024
R-4.4-mac-x86_64OKOct 31 2024
R-4.4-mac-aarch64OKOct 31 2024
R-4.3-win-x86_64OKOct 31 2024
R-4.3-mac-x86_64OKOct 31 2024
R-4.3-mac-aarch64OKOct 31 2024

Exports:asNNGraphbuildVelovizgraphViznormalizeDepthnormalizeVarianceplotEmbeddingplotVelovizprojectedNeighborsreduceDimensions

Dependencies:clicpp11glueigraphlatticelifecyclemagrittrMatrixmgcvnlmepkgconfigRcppRcppEigenrlangRSpectravctrs

VeloViz Vignette

Lyla Atta

Rendered fromvignette.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2021-07-14
Started: 2021-05-05