Package: dandelionR 1.5.0

Kelvin Tuong

dandelionR: Single-cell Immune Repertoire Trajectory Analysis in R

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.

Authors:Jiawei Yu [aut], Nicholas Borcherding [aut], Kelvin Tuong [aut, cre]

dandelionR_1.5.0.tar.gz
dandelionR_1.5.0.zip(r-4.7)dandelionR_1.5.0.zip(r-4.6)dandelionR_1.5.0.zip(r-4.5)
dandelionR_1.5.0.tgz(r-4.6-any)dandelionR_1.5.0.tgz(r-4.5-any)
dandelionR_1.5.0.tar.gz(r-4.7-any)dandelionR_1.5.0.tar.gz(r-4.6-any)
dandelionR_1.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
dandelionR/json (API)
NEWS

# Install 'dandelionR' in R:
install.packages('dandelionR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/tuonglab/dandelionr/issues

Datasets:
  • demo_airr - Example AIRR Dataset for V(D)J Analysis
  • demo_sce - Example SCE Dataset that does not contain V(D)J information
  • sce_vdj - Example Dataset for V(D)J Analysis

On BioConductor:dandelionR-1.5.0(bioc 3.24)dandelionR-1.4.0(bioc 3.23)

softwareimmunooncologysinglecell

6.10 score 12 stars 10 scripts 302 downloads 5 exports 180 dependencies

Last updated from:28f4e0c808. Checks:8 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE267
linux-devel-x86_64NOTE566
source / vignettesOK436
linux-release-x86_64NOTE472
macos-release-arm64NOTE241
macos-oldrel-arm64NOTE220
windows-develNOTE395
windows-releaseNOTE351
windows-oldrelNOTE351
wasm-releaseOK198

Exports:markovProbabilitymiloUmapprojectPseudotimeToCellsetupVdjPseudobulkvdjPseudobulk

Dependencies:abindassortheadbackportsbase64encbbotkbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularblusterbootbroomcachemcarcarDatacheckmateclasscliclustercodetoolscolorspacecowplotcpp11data.tableDelayedArrayDEoptimRDerivdestinydigestdoBydotCall64dplyrdqrnge1071edgeRevaluatefarverfastmapFNNforecastformatRFormulafracdifffutile.loggerfutile.optionsfuturefuture.applygenericsGenomicRangesggbeeswarmggforceggplot.multistatsggplot2ggraphggrepelggthemesglobalsgluegraphlayoutsgridExtragtablegtoolshexbinigraphIRangesirlbaisobandjsonliteknn.covertreelabelinglaekenlambda.rlatticelgrlifecyclelimmalistenvlme4lmtestlocfitmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmiloRminqamiraimlbenchmlr3mlr3learnersmlr3measuresmlr3miscmlr3pipelinesmlr3tuningmodelrnanonextnlmenloptrnnetnumDerivpalmerpenguinsparadoxparallellypatchworkpbkrtestpcaMethodspillarpkgconfigpolyclippracmaproxyPRROCpurrrquantregR6rangerRANNrbibutilsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRdpackreformulasrlangrobustbaseRSpectrarsvdS4ArraysS4VectorsS7ScaledMatrixscalesscatterplot3dSeqinfoSingleCellExperimentsitmosnowspspamSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsystemfontstibbletidygraphtidyrtidyselecttimeDatetweenrurcautf8uuiduwotvcdvctrsVIMviporviridisviridisLitewithrxgboostXVectorzoo

Reproducing the original dandelion method/paper

Rendered fromvignette_reproduce_original.rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2025-08-08
Started: 2024-12-13

Single-cell immune repertoire trajectory analysis with dandelionR

Rendered fromdandelionR.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2025-08-08
Started: 2025-02-07

Single-cell immune repertoire trajectory analysis with dandelionR and slingshot

Rendered fromdandelionR_with_slingshot.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2025-08-08
Started: 2025-08-08