Package: SuperCellCyto 1.2.0

Givanna Putri

SuperCellCyto: SuperCell For Cytometry Data

SuperCellCyto provides the ability to summarise cytometry data into supercells by merging together cells that are similar in their marker expressions using the SuperCell package.

Authors:Givanna Putri [aut, cre], George Howitt [aut], Felix Marsh-Wakefield [aut], Thomas Ashhurst [aut], Belinda Phipson [aut]

SuperCellCyto_1.2.0.tar.gz
SuperCellCyto_1.2.0.zip(r-4.7)SuperCellCyto_1.2.0.zip(r-4.6)SuperCellCyto_1.2.0.zip(r-4.5)
SuperCellCyto_1.2.0.tgz(r-4.6-any)SuperCellCyto_1.2.0.tgz(r-4.5-any)
SuperCellCyto_1.2.0.tar.gz(r-4.7-any)SuperCellCyto_1.2.0.tar.gz(r-4.6-any)
SuperCellCyto_1.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SuperCellCyto/json (API)

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

Bug tracker:https://github.com/phipsonlab/supercellcyto/issues

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

On BioConductor:SuperCellCyto-1.3.0(bioc 3.24)SuperCellCyto-1.2.0(bioc 3.23)

cellbiologyflowcytometrysoftwaresinglecellbioinformaticscomputational-biologycytometry

6.63 score 13 stars 22 scripts 3 exports 136 dependencies

Last updated from:ad1bb6a08b (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE244
linux-devel-x86_64OK422
source / vignettesOK359
linux-release-x86_64OK426
macos-release-arm64OK275
macos-oldrel-arm64OK245
windows-develOK375
windows-releaseOK339
windows-oldrelOK368
wasm-releaseOK246

Exports:recomputeSupercellsrunSuperCellCytosimCytoData

Dependencies:askpassbackportsbase64encBHBiocParallelbitbit64bootbroombslibcachemcheckmateclicliprclustercodetoolscolorspacecorpcorcpp11crayondata.tabledbscandigestdplyrentropyevaluatefarverfastmapfontawesomeforcatsforeachforeignformatRFormulafsfutile.loggerfutile.optionsgdatagenericsggplot2glmnetgluegridExtragtablegtoolshavenherehighrHmischmshtmlTablehtmltoolshtmlwidgetsigraphirlbaisobanditeratorsjomojquerylibjsonliteknitrlabelinglambda.rlatticelifecyclelme4magrittrMASSMatrixmatrixStatsmemoisemicemimeminqamitmlnlmenloptrnnetnumDerivopensslordinalpanpatchworkpillarpkgconfigplotfunctionsplyrpngprettyunitsprogressproxypurrrR6RANNrappdirsrbibutilsRColorBrewerRcppRcppEigenRcppTOMLRdpackreadrreformulasreticulaterlangrmarkdownrpartrprojrootRSpectrarstudioapiRtsneS7sassscalesshapesnowstringistringrSuperCellsurvivalsystibbletidyrtidyselecttinytextzdbucminfumaputf8vctrsviridisLitevroomweightswithrxfunyaml

Interoperability with SingleCellExperiment
Introduction | Preparing SCE object | Run SuperCellCyto | Analyse Supercells as SCE object | Transfer information from supercells SCE object to single cell SCE object | Session information
Rendered frominteroperability_with_sce.Rmdusingknitr::rmarkdown

Last update: 2025-10-14
Started: 2024-01-24

How to create supercells
Introduction | Installation | Preparing your dataset | Creating supercells | Supercell object | Supercell expression matrix | SuperCellId | Supercell cell map | Running runSuperCellCyto in parallel | Controlling supercells granularity | Adjusting gamma value after one run of runSuperCellCyto | Specifying different gamma value for different samples | Mixing cells from different samples in a supercell | I have more cells than RAM in my computer | Session information
Rendered fromSuperCellCyto.Rmdusingknitr::rmarkdown

Last update: 2025-09-22
Started: 2025-09-22

How to Prepare Data for SuperCellCyto
Performing Quality Control | Preparing FCS/CSV files for SuperCellCyto | Cell ID column | Sample column | Preparing CSV files | Preparing FCS files | Data Transformation | Session information
Rendered fromhow_to_prepare_data.Rmdusingknitr::rmarkdown

Last update: 2025-09-22
Started: 2024-01-19

Interoperability with Seurat
Introduction | Preparing Seurat object | Run SuperCellCyto | Analyse Supercells as Seurat object | Transfer information from supercells to single-cell Seurat object | Session information
Rendered frominteroperability_with_seurat.Rmdusingknitr::rmarkdown

Last update: 2025-09-22
Started: 2024-01-24

Using SuperCellCyto for Stratified Summarising
Session information
Rendered fromusing_supercellcyto_for_stratified_summarising.Rmdusingknitr::rmarkdown

Last update: 2025-09-22
Started: 2024-01-22