This package is considered a duplicate. The official version of this package is found at:https://qile0317.r-universe.dev/APackOfTheClones

Package: APackOfTheClones 1.2.4

Qile Yang

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_1.2.4.tar.gz
APackOfTheClones_1.2.4.tar.gz(r-4.5-noble)APackOfTheClones_1.2.4.tar.gz(r-4.4-noble)
APackOfTheClones_1.2.4.tgz(r-4.4-emscripten)APackOfTheClones_1.2.4.tgz(r-4.3-emscripten)
APackOfTheClones.pdf |APackOfTheClones.html✨
APackOfTheClones/json (API)

# Install 'APackOfTheClones' in R:

install.packages('APackOfTheClones', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

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

3.40 score 7 scripts 346 downloads 19 exports 151 dependencies

Last updated 6 days agofrom:cb5bfc024f. Checks:OK: 2. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Nov 19 2024
R-4.5-linux-x86_64	OK	Nov 19 2024

Exports:AdjustAPOTC APOTCPlot clonal_expansion_plot containsApotcRun count_clone_sizes countCloneSizes deleteApotcData getApotcDataIds getLastApotcDataId getReductionCentroids getSharedClones integrate_tcr mergeCloneSizes overlayLegend removeLegend renameApotcRun RunAPOTC showCloneHighlight vizAPOTC

Dependencies:abind askpass assertthat base64enc BH bitops bslib cachem caTools cli cluster codetools colorspace commonmark cowplot cpp11 crayon crosstalk curl data.table deldir digest dotCall64 dplyr dqrng evaluate fansi farver fastDummies fastmap fitdistrplus FNN fontawesome fs future future.apply generics ggforce ggplot2 ggrepel ggridges globals glue goftest gplots gridExtra gtable gtools hash here highr htmltools htmlwidgets httpuv httr ica igraph irlba isoband jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval leiden lifecycle listenv lmtest magrittr MASS Matrix matrixStats memoise mgcv mime miniUI munsell nlme openssl parallelly patchwork pbapply pillar pkgconfig plotly plyr png polyclip progressr promises purrr R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppProgress RcppTOML reshape2 reticulate rlang rmarkdown ROCR rprojroot RSpectra Rtsne sass scales scattermore sctransform Seurat SeuratObject shiny sitmo sourcetools sp spam spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringi stringr survival sys systemfonts tensor tibble tidyr tidyselect tinytex tweenr utf8 uwot vctrs viridisLite withr xfun xtable yaml zoo

APackOfTheClones Essentials

Rendered fromAPackOfTheClones.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2024-10-10
Started: 2024-01-14

Clonal Analysis Utilities in APackOfTheClones

Rendered fromAPackOfTheClones-utils.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2024-10-10
Started: 2024-04-06

Installing APackOfTheClones

Rendered fromAPackOfTheClones-install.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2024-10-10
Started: 2024-04-06

Storing and Fine-Tuning APackOfTheClones Runs

Rendered fromAPackOfTheClones-runs.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2024-10-10
Started: 2024-01-14

Working With Clonotypes Shared Across Clusters

Rendered fromAPackOfTheClones-shared.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2024-10-10
Started: 2024-04-06

Citation

Readme and manuals

Help Manual

Help page	Topics
Adjust the parameters of the APackOfTheClones reduction in a seurat object	AdjustAPOTC
Various variations of visualizations of clonal expansion post-RunAPOTC	APOTCPlot
Example Multi-sampled T-cell seurat object with integrated TCR library	combined_pbmc
Check for the existence of an APackOfTheClones run with its run id	containsApotcRun
count the number of clonotype sizes in a seurat object combined with a VDJ library overall or by cluster	countCloneSizes
Delete the results of an APackOfTheClones run	deleteApotcData
Get all run ids of previous RunAPOTC runs on a seurat object	getApotcDataIds
Get the object id of the most recent RunAPOTC run on a seurat object	getLastApotcDataId
Calculate seurat cluster centroids based on a Dimensional reduction	getReductionCentroids
Compute a list of clonotypes that are shared between seurat clusters	getSharedClones
Merge a list of Clustered Clonotype Frequency Tables	mergeCloneSizes
overlay a clone size legend on an APackOfTheClones plot	overlayLegend
Remove current APackOfTheClones legend	removeLegend
Rename an APackOfTheClones run	renameApotcRun
Run the APackOfTheClones method on a combined Seurat object for downstream visualization of clonal expansion	RunAPOTC
Highlight specific clones on an APackOfTheClones ggplot	showCloneHighlight
Directly visualize clonal expansion of a combined seurat object	vizAPOTC

Package: APackOfTheClones 1.2.4

APackOfTheClones: Visualization of Clonal Expansion for Single Cell Immune Profiles

APackOfTheClones Essentials

Clonal Analysis Utilities in APackOfTheClones

Installing APackOfTheClones

Storing and Fine-Tuning APackOfTheClones Runs

Working With Clonotypes Shared Across Clusters

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)