Package: dandelionR
Title: Single-cell Immune Repertoire Trajectory Analysis in R
Version: 1.3.0
Authors@R:
    c(person(given="Jiawei", family="Yu", email = "jiawei.yu@uq.edu.au", role = c("aut"), comment = c(ORCID = "0009-0005-9170-7881")),
      person(given="Nicholas", family="Borcherding", email = "borcherding@wustl.edu", role = c("aut"), comment = c(ORCID = "0000-0003-1427-6342")),
      person(given="Kelvin", family="Tuong", email = "z.tuong@uq.edu.au", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6735-6808")))
Description: dandelionR is an R package for performing single-cell immune repertoire trajectory analysis, based on the original python implementation. It provides the necessary functions to interface with scRepertoire and a custom implementation of an absorbing Markov chain for pseudotime inference, inspired by the Palantir Python package.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
biocViews: Software, ImmunoOncology, SingleCell
Collate:
    'check.R'
    'constructMarkovChain.R'
    'dandelionR.R'
    'data.R'
    'determMultiscaleSpace.R'
    'terminalStateFromMarkovChain.R'
    'differentiationProbabilities.R'
    'filterCells.R'
    'getPbs.R'
    'projectProbability.R'
    'maxMinSampling.R'
    'minMaxScale.R'
    'markovProbability.R'
    'miloUmap.R'
    'projectPseudotimeToCell.R'
    'setupVdjPseudobulk.R'
    'splitCTgene.R'
    'vdjPseudobulk.R'
Imports:
    BiocGenerics,
    bluster,
    destiny, 
    igraph,
    MASS,
    Matrix,
    methods,
    miloR,
    purrr,
    rlang,
    S4Vectors,
    SingleCellExperiment,
    spam,
    stats,
    SummarizedExperiment,
    uwot,
    RANN
Suggests:
    BiocStyle,
    fields,
    knitr,
    rmarkdown,
    RColorBrewer,
    scater,
    scRepertoire,
    DelayedMatrixStats,
    slingshot,
    testthat
VignetteBuilder: knitr
URL: https://www.github.com/tuonglab/dandelionR/
BugReports: https://www.github.com/tuonglab/dandelionR/issues
Depends: 
    R (>= 4.4.0)
git_url: https://git.bioconductor.org/packages/dandelionR
git_branch: devel
git_last_commit: 29dd237
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
