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DESCRIPTION
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DESCRIPTION
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Package: veloviz
Title: VeloViz: RNA-velocity informed 2D embeddings for visualizing cell state trajectories
Version: 1.2.1
Authors@R:
c(person(given = "Lyla",
family = "Atta",
role = c("aut", "cre"),
email = "[email protected]",
comment = c(ORCID = "0000-0002-6113-0082")),
person(given = "Jean",
family = "Fan",
role = c("aut"),
email = "[email protected]",
comment = c(ORCID = "0000-0002-0212-5451")),
person(given = "Arpan",
family = "Sahoo",
role = c("aut"),
email = "[email protected]",
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