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✨
DESCRIPTION |NEWS
card.svg |card.png
dandelionR/json (API)

# 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

5.95 score 12 stars 10 scripts 260 downloads 5 exports 180 dependencies

Last updated from:28f4e0c808. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING278
linux-devel-x86_64NOTE544
source / vignettesOK468
linux-release-x86_64NOTE535
macos-release-arm64NOTE234
macos-oldrel-arm64NOTE271
windows-develNOTE379
windows-releaseNOTE405
windows-oldrelNOTE383
wasm-releaseOK234

Exports:markovProbabilitymiloUmapprojectPseudotimeToCellsetupVdjPseudobulkvdjPseudobulk

Dependencies:abindassortheadbackportsbase64encbbotkbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularblusterbootbroomcachemcarcarDatacheckmateclasscliclustercodetoolscolorspacecowplotcpp11data.tableDelayedArrayDEoptimRDerivdestinydigestdoBydotCall64dplyrdqrnge1071edgeRevaluatefarverfastmapFNNforecastformatRFormulafracdifffutile.loggerfutile.optionsfuturefuture.applygenericsGenomicRangesggbeeswarmggforceggplot.multistatsggplot2ggraphggrepelggthemesglobalsgluegraphlayoutsgridExtragtablegtoolshexbinigraphIRangesirlbaisobandjsonliteknn.covertreelabelinglaekenlambda.rlatticelgrlifecyclelimmalistenvlme4lmtestlocfitmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmiloRminqamiraimlbenchmlr3mlr3learnersmlr3measuresmlr3miscmlr3pipelinesmlr3tuningmodelrmoocorenanonextnlmenloptrnnetnumDerivpalmerpenguinsparadoxparallellypatchworkpbkrtestpcaMethodspillarpkgconfigpolyclippracmaproxyPRROCpurrrquantregR6rangerRANNrbibutilsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRdpackreformulasrlangrobustbaseRSpectrarsvdS4ArraysS4VectorsS7ScaledMatrixscalesscatterplot3dSeqinfoSingleCellExperimentsitmosnowspspamSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsystemfontstibbletidygraphtidyrtidyselecttimeDatetweenrurcautf8uuiduwotvcdvctrsVIMviporviridisviridisLitewithrxgboostXVectorzoo

Reproducing the original dandelion method/paper
Load the required libraries | Load data | Filter the data | Milo object and neighbourhood graph construction | Construct UMAP on milo neighbor graph | Construct pseudobulked VDJ feature space | TCR trajectory inference using Absorbing Markov Chain | Define root and branch tips | Construct diffusion map | Compute diffussion pseudotime on diffusion map | Markov chain construction on the pseudobulk VDJ feature space | Visualising branch probabilities | Transfer | Project pseudobulk data to each cell | Visualise the trajectory data on a per cell basis | Session info
Rendered fromvignette_reproduce_original.rmdusingknitr::rmarkdown

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

Single-cell immune repertoire trajectory analysis with dandelionR
Foreword | Installation | Bioconductor | Development version (GitHub) | Usage | Load the required libraries | Load the demo data | Use scRepertoire to load the VDJ data | Merging VDJ data with gene expression data | Initiate dandelionR workflow | Milo object and neighbourhood graph construction | Construct UMAP on milo neighbor graph | Construct pseudobulked VDJ feature space | TCR trajectory inference using Absorbing Markov Chain | Define root and branch tips | Construct diffusion map | Compute diffusion pseudotime on diffusion map | Markov chain construction on the pseudobulk VDJ feature space | Visualising branch probabilities | Transfer | Project pseudobulk data to each cell | Visualise the trajectory data on a per cell basis | Session info
Rendered fromdandelionR.Rmdusingknitr::rmarkdown

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

Single-cell immune repertoire trajectory analysis with dandelionR and slingshot
Foreword | Installing slinshot | Load the required libraries and data | Setup the data as per the other vignettes | Milo object and neighbourhood graph construction | Construct UMAP on milo neighbor graph | Construct pseudobulked VDJ feature space | TCR trajectory inference using Slingshot | input | run slingshot | Visualization | Transfer | Project pseudobulk data to each cell | Visualise the trajectory data on a per cell basis | Session info
Rendered fromdandelionR_with_slingshot.Rmdusingknitr::rmarkdown

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