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

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2.30 score 4 scripts 139 downloads 6 exports 148 dependencies

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

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Doc / VignettesOKDec 12 2024
R-4.5-linuxWARNINGDec 12 2024

Exports:%>%genesetCytoSiggenesetReactomescapescapeForSeuratsupportedCytokines

Dependencies:abindaskpassbase64encBHbitopsbslibcachemcaToolscliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tabledeldirdigestdotCall64dplyrdqrngevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomefsfuturefuture.applygenericsggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleidenlifecyclelistenvlmtestmagrittrMASSMatrixmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRtsnesassscalesscattermoresctransformSeuratSeuratObjectshinysitmosourcetoolsspspamspatstat.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 Dec 12 2024.

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 Dec 12 2024.

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