Package: veloviz
Title: VeloViz: RNA-velocity informed 2D embeddings for visualizing
        cell state trajectories
Version: 1.16.0
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
Config/pak/sysreqs: libglpk-dev libxml2-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:11:22 UTC
RemoteUrl: https://github.com/bioc/veloviz
RemoteRef: RELEASE_3_22
RemoteSha: 97d9beb72d323b2b09553d5310841614394c992b
NeedsCompilation: yes
Packaged: 2025-11-11 18:10:46 UTC; root
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 4.5.2; x86_64-w64-mingw32; 2025-11-11 18:13:53 UTC; windows
Archs: x64
