Package: APackOfTheClones 1.2.1

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_1.2.1.tar.gz
APackOfTheClones_1.2.1.zip(r-4.5)APackOfTheClones_1.2.1.zip(r-4.4)APackOfTheClones_1.2.1.zip(r-4.3)
APackOfTheClones_1.2.1.tgz(r-4.4-x86_64)APackOfTheClones_1.2.1.tgz(r-4.4-arm64)APackOfTheClones_1.2.1.tgz(r-4.3-x86_64)APackOfTheClones_1.2.1.tgz(r-4.3-arm64)
APackOfTheClones_1.2.1.tar.gz(r-4.5-noble)APackOfTheClones_1.2.1.tar.gz(r-4.4-noble)
APackOfTheClones_1.2.1.tgz(r-4.4-emscripten)APackOfTheClones_1.2.1.tgz(r-4.3-emscripten)
APackOfTheClones.pdf |APackOfTheClones.html✨
APackOfTheClones/json (API)

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

Peer review:

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

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

On CRAN:

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

6.66 score 14 stars 11 scripts 301 downloads 19 exports 151 dependencies

Last updated 11 days agofrom:3eee57292c. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 10 2024
R-4.5-win-x86_64OKOct 10 2024
R-4.5-linux-x86_64OKOct 10 2024
R-4.4-win-x86_64OKOct 10 2024
R-4.4-mac-x86_64OKOct 10 2024
R-4.4-mac-aarch64OKOct 10 2024
R-4.3-win-x86_64OKOct 10 2024
R-4.3-mac-x86_64OKOct 10 2024
R-4.3-mac-aarch64OKOct 10 2024

Exports:AdjustAPOTCAPOTCPlotclonal_expansion_plotcontainsApotcRuncount_clone_sizescountCloneSizesdeleteApotcDatagetApotcDataIdsgetLastApotcDataIdgetReductionCentroidsgetSharedClonesintegrate_tcrmergeCloneSizesoverlayLegendremoveLegendrenameApotcRunRunAPOTCshowCloneHighlightvizAPOTC

Dependencies:abindaskpassassertthatbase64encBHbitopsbslibcachemcaToolscliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tabledeldirdigestdotCall64dplyrdqrngevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomefsfuturefuture.applygenericsggforceggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolshashherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleidenlifecyclelistenvlmtestmagrittrMASSMatrixmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRtsnesassscalesscattermoresctransformSeuratSeuratObjectshinysitmosourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivalsyssystemfontstensortibbletidyrtidyselecttinytextweenrutf8uwotvctrsviridisLitewithrxfunxtableyamlzoo

APackOfTheClones Essentials

Rendered fromAPackOfTheClones.Rmdusingknitr::rmarkdownon Oct 10 2024.

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

Clonal Analysis Utilities in APackOfTheClones

Rendered fromAPackOfTheClones-utils.Rmdusingknitr::rmarkdownon Oct 10 2024.

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

Installing APackOfTheClones

Rendered fromAPackOfTheClones-install.Rmdusingknitr::rmarkdownon Oct 10 2024.

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

Storing and Fine-Tuning APackOfTheClones Runs

Rendered fromAPackOfTheClones-runs.Rmdusingknitr::rmarkdownon Oct 10 2024.

Last update: 2024-10-10
Started: 2024-01-06

Working With Clonotypes Shared Across Clusters

Rendered fromAPackOfTheClones-shared.Rmdusingknitr::rmarkdownon Oct 10 2024.

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