Package: veloviz
Title: VeloViz: RNA-velocity informed 2D embeddings for visualizing
        cell state trajectories
Version: 1.15.0
Authors@R: 
    c(person(given = "Lyla",
           family = "Atta",
           role = c("aut", "cre"),
           email = "lylaatta@jhmi.edu",
           comment = c(ORCID = "0000-0002-6113-0082")),
           person(given = "Jean",
                  family = "Fan",
                  role = c("aut"),
                  email = "jeanfan@jhu.edu",
                  comment = c(ORCID = "0000-0002-0212-5451")),
           person(given = "Arpan",
                  family = "Sahoo",
                  role = c("aut"),
                  email = "asahoo1@jhu.edu",
                  comment = c(ORCID = "0000-0002-0325-2073")))
Description: 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.
biocViews: Transcriptomics, Visualization, GeneExpression, Sequencing,
        RNASeq, DimensionReduction
License: GPL-3
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
Imports: Rcpp, Matrix, igraph, mgcv, RSpectra, grDevices, graphics,
        stats
LinkingTo: Rcpp
Depends: R (>= 4.1)
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/veloviz
git_branch: devel
git_last_commit: 34ad57c
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-06-04
NeedsCompilation: yes
Packaged: 2025-06-05 02:45:29 UTC; biocbuild
Author: Lyla Atta [aut, cre] (ORCID: <https://orcid.org/0000-0002-6113-0082>),
  Jean Fan [aut] (ORCID: <https://orcid.org/0000-0002-0212-5451>),
  Arpan Sahoo [aut] (ORCID: <https://orcid.org/0000-0002-0325-2073>)
Maintainer: Lyla Atta <lylaatta@jhmi.edu>
Built: R 4.5.0; x86_64-w64-mingw32; 2025-06-05 14:17:42 UTC; windows
Archs: x64
