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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>.
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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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Last updated 1 years agofrom:c142447718. Checks:OK: 1 WARNING: 1. Indexed: yes.
Target | Result | Date |
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Doc / Vignettes | OK | Oct 13 2024 |
R-4.5-linux | WARNING | Oct 13 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.
Rendered fromscaper-vignette-CytoSig.Rmd
usingknitr::rmarkdown
on Oct 13 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.
Rendered fromscaper-vignette-Reactome.Rmd
usingknitr::rmarkdown
on Oct 13 2024.Last update: 2023-10-19
Started: 2023-10-19
Readme and manuals
Help Manual
Help page | Topics |
---|---|
CytoSig gene set construction. | genesetCytoSig |
Reactome gene set construction. | genesetReactome |
Cytokine activity scores for a normalized matrix. | scape |
Cytokine activity scores for a Seurat matrix. | scapeForSeurat |
Gene set to score for the CytoSig or the Reactome databases. | supportedCytokines |