Package: dandelionR 0.99.10
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:
dandelionR_0.99.10.tar.gz
dandelionR_0.99.10.zip(r-4.5)dandelionR_0.99.10.zip(r-4.4)
dandelionR_0.99.10.tgz(r-4.5-any)dandelionR_0.99.10.tgz(r-4.4-any)
dandelionR_0.99.10.tar.gz(r-4.5-noble)dandelionR_0.99.10.tar.gz(r-4.4-noble)
dandelionR_0.99.10.tgz(r-4.4-emscripten)
dandelionR.pdf |dandelionR.html✨
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
On BioConductor:dandelionR-0.99.10(bioc 3.21)
softwareimmunooncologysinglecell
Last updated 7 days agofrom:4b4b57bcdf. Checks:6 OK. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 22 2025 |
| R-4.5-win | OK | Feb 22 2025 |
| R-4.5-mac | OK | Feb 22 2025 |
| R-4.5-linux | OK | Feb 22 2025 |
| R-4.4-win | OK | Feb 22 2025 |
| R-4.4-mac | OK | Feb 22 2025 |
Exports:markovProbabilitymiloUmapprojectPseudotimeToCellsetupVdjPseudobulkvdjPseudobulk
Dependencies:abindaskpassassortheadbackportsbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularblusterbootbroomcachemcarcarDataclasscliclustercodetoolscolorspacecowplotcpp11crayoncurldata.tableDelayedArrayDEoptimRDerivdestinydoBydotCall64dplyrdqrnge1071edgeRfansifarverfastmapFNNformatRFormulafutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggforceggplot.multistatsggplot2ggraphggrepelggthemesgluegraphlayoutsgridExtragtablegtoolshexbinhttrigraphIRangesirlbaisobandjsonliteknn.covertreelabelinglaekenlambda.rlatticelifecyclelimmalme4lmtestlocfitmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmiloRmimeminqamodelrmunsellnlmenloptrnnetnumDerivopensslpatchworkpbkrtestpcaMethodspillarpkgconfigpolyclippracmaproxypurrrquantregR6rangerrbibutilsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppMLRcppProgressRdpackreformulasrlangrobustbaseRSpectrarsvdS4ArraysS4VectorsScaledMatrixscalesscatterplot3dSingleCellExperimentsitmosmoothersnowspspamSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstibbletidygraphtidyrtidyselectTTRtweenrUCSC.utilsutf8uwotvcdvctrsVIMviporviridisviridisLitewithrxtsXVectorzoo
Reproducing the original dandelion method/paper
Rendered fromvignette_reproduce_original.rmdusingknitr::rmarkdownon Feb 22 2025.Last update: 2025-02-08
Started: 2024-12-13
Single-cell immune repertoire trajectory analysis with dandelionR
Rendered fromdandelionR.Rmdusingknitr::rmarkdownon Feb 22 2025.Last update: 2025-02-14
Started: 2025-02-07
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Example AIRR Dataset for V(D)J Analysis | demo_airr |
| Example SCE Dataset that does not contain V(D)J information | demo_sce |
| Compute Branch Probabilities Using Markov Chain | differentiationProbabilities |
| Markov Chain Construction and Probability Calculation | markovProbability |
| Perform UMAP on the Adjacency Matrix of a Milo Object | miloUmap |
| Project Probabilities from Markov Chain to Pseudobulks | projectProbability |
| Project Pseudotime and Branch Probabilities to Single Cells | projectPseudotimeToCell |
| Example Dataset for V(D)J Analysis | sce_vdj |
| Preprocess V(D)J Data for Pseudobulk Analysis | setupVdjPseudobulk |
| Generate Pseudobulk V(D)J Feature Space | vdjPseudobulk |
