Package: APackOfTheClones 1.2.0

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_1.2.0.tar.gz
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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

19 exports 13 stars 2.32 score 149 dependencies 251 downloads

Last updated 3 months agofrom:2e135efd8a

Exports:AdjustAPOTCAPOTCPlotclonal_expansion_plotcontainsApotcRuncount_clone_sizescountCloneSizesdeleteApotcDatagetApotcDataIdsgetLastApotcDataIdgetReductionCentroidsgetSharedClonesintegrate_tcrmergeCloneSizesoverlayLegendremoveLegendrenameApotcRunRunAPOTCshowCloneHighlightvizAPOTC

Dependencies:abindaskpassbase64encBHbitopsbslibcachemcaToolscliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tabledeldirdigestdotCall64dplyrdqrngevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomefsfuturefuture.applygenericsggforceggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolshashherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleidenlifecyclelistenvlmtestmagrittrMASSMatrixmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRtsnesassscalesscattermoresctransformSeuratSeuratObjectshinysitmosourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.utilsstringistringrsurvivalsyssystemfontstensortibbletidyrtidyselecttinytextweenrutf8uwotvctrsviridisLitewithrxfunxtableyamlzoo

APackOfTheClones Essentials

Rendered fromAPackOfTheClones.Rmdusingknitr::rmarkdownon Jun 25 2024.

Last update: 2024-04-16
Started: 2024-01-10

Clonal Analysis Utilities in APackOfTheClones

Rendered fromAPackOfTheClones-utils.Rmdusingknitr::rmarkdownon Jun 25 2024.

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

Installing APackOfTheClones

Rendered fromAPackOfTheClones-install.Rmdusingknitr::rmarkdownon Jun 25 2024.

Last update: 2024-04-16
Started: 2024-04-05

Storing and Fine-Tuning APackOfTheClones Runs

Rendered fromAPackOfTheClones-runs.Rmdusingknitr::rmarkdownon Jun 25 2024.

Last update: 2024-04-16
Started: 2024-01-06

Working With Clonotypes Shared Across Clusters

Rendered fromAPackOfTheClones-shared.Rmdusingknitr::rmarkdownon Jun 25 2024.

Last update: 2024-04-16
Started: 2024-04-05