Package: scaper 0.2.1

scaper: Single Cell Transcriptomics-Level Cytokine Activity Prediction and Estimation

Generates cell-level cytokine activity estimates using relevant information from gene sets constructed with the 'CytoSig' and the 'Reactome' databases and scored using the modified 'Variance-adjusted Mahalanobis (VAM)' framework for single-cell RNA-sequencing (scRNA-seq) data. 'CytoSig' database is described in: Jiang at al., (2021) <doi:10.1038/s41592-021-01274-5>. 'Reactome' database is described in: Gillespie et al., (2021) <doi:10.1093/nar/gkab1028>. The 'VAM' method is outlined in: Frost (2020) <doi:10.1093/nar/gkaa582>.

Authors:Zaoqu Liu [aut, cre], H. Robert Frost [aut], Azka Javaid [aut]

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

Bug tracker:https://github.com/zaoqu-liu/scaper/issues

On CRAN:

Conda:

3.51 score 13 scripts 564 downloads 6 exports 143 dependencies

Last updated from:76fae1d8a4 (on main). Checks:9 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK238
source / vignettesOK275
linux-release-x86_64OK247
macos-release-arm64OK118
macos-oldrel-arm64OK116
windows-develOK181
windows-releaseOK215
windows-oldrelOK281
wasm-releaseOK165

Exports:%>%genesetCytoSiggenesetReactomescapescapeForSeuratsupportedCytokines

Dependencies:abindaskpassbase64encBHbitopsbslibcachemcaToolscliclustercodetoolscommonmarkcowplotcpp11crosstalkcurldata.tabledeldirdigestdotCall64dplyrdqrngevaluatefarverfastDummiesfastmapfitdistrplusFNNfontawesomefsfuturefuture.applygenericsggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallifecyclelistenvlmtestmagrittrMASSMatrixmatrixStatsmemoisemimeminiUInlmeopensslotelparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRtsneS7sassscalesscattermoresctransformSeuratSeuratObjectshinysitmosourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivalsystensortibbletidyrtidyselecttinytexutf8uwotvctrsviridisLitewithrxfunxml2xtableyamlzoo

Algorithm Details: Mathematical Foundation of scaper

Zaoqu Liu

Rendered fromalgorithm-details.Rmdusingknitr::rmarkdownon May 25 2026.

Last update: 2026-01-25
Started: 2026-01-25

Introduction to scaper: Cytokine Activity Estimation in Single Cells

Zaoqu Liu

Rendered fromintroduction.Rmdusingknitr::rmarkdownon May 25 2026.

Last update: 2026-01-25
Started: 2026-01-25

Cytokine Activity Estimation using SCAPE (Single cell transcriptomics-level Cytokine Activity Prediction and Estimation): An Analysis using the CytoSig database.

Zaoqu Liu, Azka Javaid and H. Robert Frost

Rendered fromscaper-vignette-CytoSig.Rmdusingknitr::rmarkdownon May 25 2026.

Last update: 2026-01-25
Started: 2026-01-25

Cytokine Activity Estimation using SCAPE (Single cell transcriptomics-level Cytokine Activity Prediction and Estimation): An Analysis using the Reactome database.

Zaoqu Liu, Azka Javaid and H. Robert Frost

Rendered fromscaper-vignette-Reactome.Rmdusingknitr::rmarkdownon May 25 2026.

Last update: 2026-01-25
Started: 2026-01-25

Visualization Guide for scaper

Zaoqu Liu

Rendered fromvisualization.Rmdusingknitr::rmarkdownon May 25 2026.

Last update: 2026-01-25
Started: 2026-01-25