Package: APackOfTheClones 1.3.0

APackOfTheClones: Visualization of Clonal Expansion for Single Cell Immune Profiles

Visualize clonal expansion via circle-packing. 'APackOfTheClones' extends 'scRepertoire' to produce a publication-ready visualization of clonal expansion at a single cell resolution, by representing expanded clones as differently sized circles. The method was originally implemented by Murray Christian and Ben Murrell in the following immunology study: Ma et al. (2021) <doi:10.1126/sciimmunol.abg6356>.

Authors:Qile Yang [cre, aut, cph]

APackOfTheClones_1.3.0.tar.gz
APackOfTheClones_1.3.0.zip(r-4.7)APackOfTheClones_1.3.0.zip(r-4.6)APackOfTheClones_1.3.0.zip(r-4.5)
APackOfTheClones_1.3.0.tgz(r-4.6-x86_64)APackOfTheClones_1.3.0.tgz(r-4.6-arm64)APackOfTheClones_1.3.0.tgz(r-4.5-x86_64)APackOfTheClones_1.3.0.tgz(r-4.5-arm64)
APackOfTheClones_1.3.0.tar.gz(r-4.7-arm64)APackOfTheClones_1.3.0.tar.gz(r-4.7-x86_64)APackOfTheClones_1.3.0.tar.gz(r-4.6-arm64)APackOfTheClones_1.3.0.tar.gz(r-4.6-x86_64)
APackOfTheClones_1.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
APackOfTheClones/json (API)

# Install 'APackOfTheClones' in R:
install.packages('APackOfTheClones', repos = c('https://qile0317.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/qile0317/apackoftheclones/issues

Pkgdown/docs site:https://qile0317.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • combined_pbmc - Example Multi-sampled T-cell seurat object with integrated TCR library

On CRAN:

Conda:

clonal-analysisimmune-repertoireimmune-systemscrna-seqscrnaseqseuratsingle-cellsingle-cell-genomicscpp

6.06 score 21 stars 11 scripts 654 downloads 22 exports 147 dependencies

Last updated from:19db788d9f. Checks:2 ERROR, 11 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64ERROR254
linux-devel-x86_64OK256
source / vignettesOK329
linux-release-arm64ERROR256
linux-release-x86_64OK275
macos-release-arm64OK198
macos-release-x86_64OK466
macos-oldrel-arm64OK189
macos-oldrel-x86_64OK433
windows-develOK277
windows-releaseOK238
windows-oldrelOK234
wasm-releaseOK177

Exports:AdjustAPOTCAPOTCPlotclonal_expansion_plotcontainsApotcRuncount_clone_sizescountCloneSizesdeleteApotcDatagetApotcDataIdsgetApotcRunIdsgetLastApotcDataIdgetLastApotcRunIdgetReductionCentroidsgetSharedClonesintegrate_tcrmergeCloneSizesoverlayLegendremoveLegendrenameApotcRunRunAPOTCshowCloneHighlightupdateApotcvizAPOTC

Dependencies:abindaskpassassertthatbase64encBHbitopsbslibcachemcaToolscliclustercodetoolscommonmarkcowplotcpp11crosstalkcurldata.tabledeldirdigestdotCall64dplyrdqrngevaluatefarverfastDummiesfastmapfitdistrplusFNNfontawesomefsfuturefuture.applygenericsggforceggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolshashherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallifecyclelistenvlmtestmagrittrMASSMatrixmatrixStatsmemoisemimeminiUInlmeopensslotelparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRtsneS7sassscalesscattermoresctransformSeuratSeuratObjectshinysitmosourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivalsyssystemfontstensortibbletidyrtidyselecttinytextweenrutf8uwotvctrsviridisLitewithrxfunxtableyamlzoo

APackOfTheClones Essentials

Rendered fromAPackOfTheClones.Rmdusingknitr::rmarkdownon May 25 2026.

Last update: 2024-10-10
Started: 2024-01-10

Clonal Analysis Utilities in APackOfTheClones

Rendered fromAPackOfTheClones-utils.Rmdusingknitr::rmarkdownon May 25 2026.

Last update: 2024-10-10
Started: 2024-04-05

Installing APackOfTheClones

Rendered fromAPackOfTheClones-install.Rmdusingknitr::rmarkdownon May 25 2026.

Last update: 2024-10-10
Started: 2024-04-05

Storing and Fine-Tuning APackOfTheClones Runs

Rendered fromAPackOfTheClones-runs.Rmdusingknitr::rmarkdownon May 25 2026.

Last update: 2025-08-18
Started: 2024-01-06

Working With Clonotypes Shared Across Clusters

Rendered fromAPackOfTheClones-shared.Rmdusingknitr::rmarkdownon May 25 2026.

Last update: 2024-10-10
Started: 2024-04-05