Package: veloviz
Title: VeloViz: RNA-velocity informed 2D embeddings for visualizing cell state trajectories
Version: 1.17.0
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: 3dd61ba
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
