Package: scaper 0.1.0

Azka Javaid

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

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

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2.30 score 174 downloads 6 exports 148 dependencies

Last updated 1 years agofrom:c142447718. Checks:1 OK, 2 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 12 2025
R-4.5-linuxWARNINGMar 12 2025
R-4.4-linuxWARNINGMar 12 2025

Exports:%>%genesetCytoSiggenesetReactomescapescapeForSeuratsupportedCytokines

Dependencies:abindaskpassbase64encBHbitopsbslibcachemcaToolscliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tabledeldirdigestdotCall64dplyrdqrngevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomefsfuturefuture.applygenericsggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleidenbaselifecyclelistenvlmtestmagrittrMASSMatrixmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRtsnesassscalesscattermoresctransformSeuratSeuratObjectshinysitmosourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivalsystensortibbletidyrtidyselecttinytexutf8uwotVAMvctrsviridisLitewithrxfunxml2xtableyamlzoo

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

Azka Javaid and H. Robert Frost

Rendered fromscaper-vignette-CytoSig.Rmdusingknitr::rmarkdownon Mar 12 2025.

Last update: 2023-10-19
Started: 2023-10-19

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

Azka Javaid and H. Robert Frost

Rendered fromscaper-vignette-Reactome.Rmdusingknitr::rmarkdownon Mar 12 2025.

Last update: 2023-10-19
Started: 2023-10-19

Citation

To cite package ‘scaper’ in publications use:

Frost H, Javaid A (2023). scaper: Single Cell Transcriptomics-Level Cytokine Activity Prediction and Estimation. R package version 0.1.0, https://CRAN.R-project.org/package=scaper.

Corresponding BibTeX entry: 

  @Manual{,
    title = {scaper: Single Cell Transcriptomics-Level Cytokine
      Activity Prediction and Estimation},
    author = {H. Robert Frost and Azka Javaid},
    year = {2023},
    note = {R package version 0.1.0},
    url = {https://CRAN.R-project.org/package=scaper},
  }