Package: escape 2.3.0

Nick Borcherding

escape: Easy single cell analysis platform for enrichment

A bridging R package to facilitate gene set enrichment analysis (GSEA) in the context of single-cell RNA sequencing. Using raw count information, Seurat objects, or SingleCellExperiment format, users can perform and visualize ssGSEA, GSVA, AUCell, and UCell-based enrichment calculations across individual cells.

Authors:Nick Borcherding [aut, cre], Jared Andrews [aut], Alexei Martsinkovskiy [ctb]

escape_2.3.0.tar.gz
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escape_2.3.0.tgz(r-4.5-any)escape_2.3.0.tgz(r-4.4-any)escape_2.3.0.tgz(r-4.3-any)
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escape_2.3.0.tgz(r-4.4-emscripten)
escape.pdf |escape.html
escape/json (API)
NEWS

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

On BioConductor:escape-2.3.0(bioc 3.21)escape-2.2.3(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

softwaresinglecellclassificationannotationgenesetenrichmentsequencinggenesignalingpathways

5.92 score 138 scripts 803 downloads 12 exports 163 dependencies

Last updated 1 months agofrom:4d1d12ed5e. Checks:2 OK, 1 FAILURE, 5 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 24 2025
R-4.5-winNOTEFeb 24 2025
R-4.5-macNOTEFeb 24 2025
R-4.5-linuxNOTEFeb 24 2025
R-4.4-winNOTEFeb 24 2025
R-4.4-macNOTEFeb 24 2025
R-4.3-winOKFeb 24 2025
R-4.3-macOUTDATEDDec 29 2024

Exports:densityEnrichmentescape.matrixgetGeneSetsgeyserEnrichmentheatmapEnrichmentpcaEnrichmentperformNormalizationperformPCAridgeEnrichmentrunEscapescatterEnrichmentsplitEnrichment

Dependencies:abindannotateAnnotationDbiaskpassassortheadAUCellbabelgenebase64encbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocNeighborsBiocParallelBiocSingularBiostringsbitbit64blobbslibcachemclicodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdigestdistributionaldotCall64dplyrevaluatefansifarverfastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggdistggplot2ggpointdensityggridgesglobalsgluegraphGSEABaseGSVAgtableh5mreadHDF5ArrayhighrhtmltoolshtmlwidgetshttrIRangesirlbaisobandjquerylibjsonliteKEGGRESTkernlabknitrlabelinglambda.rlaterlatticelazyevallifecyclelistenvmagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemixtoolsmsigdbrmunsellnlmenumDerivopensslparallellypatchworkpillarpkgconfigplogrplotlyplyrpngprogressrpromisespurrrquadprogR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppEigenreshape2rhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownRSQLitersvdS4ArraysS4VectorssassScaledMatrixscalessegmentedSeuratObjectSingleCellExperimentsnowspspamSparseArraysparseMatrixStatsSpatialExperimentstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytexUCellUCSC.utilsutf8vctrsviridisLitewithrxfunXMLxtableXVectoryaml

Using escape to perform gene set enrichment analyses on single-cell RNA-seq data

Rendered fromvignette.Rmdusingknitr::rmarkdownon Feb 24 2025.

Last update: 2025-01-24
Started: 2020-06-04