Package: CSOA 1.3.1

Andrei-Florian Stoica

CSOA: Calculate per-cell gene signature scores in scRNA-seq data using cell set overlaps

Cell Set Overlap Analysis (CSOA) is a tool for calculating per-cell gene signature scores in an scRNA-seq dataset. CSOA constructs a set for each gene in the signature, consisting of the cells that highly express the gene. Next, all overlaps of pairs of cell sets are computed, ranked, filtered and scored. The CSOA per-cell score is calculated by summing up all products of the overlap scores and the min-max-normalized expression of the two involved genes. CSOA can run on a Seurat object, a SingleCellExperiment object, a matrix and a dgCMatrix.

Authors:Andrei-Florian Stoica [aut, cre]

CSOA_1.3.1.tar.gz
CSOA_1.3.1.zip(r-4.7)CSOA_1.3.1.zip(r-4.6)CSOA_1.3.1.zip(r-4.5)
CSOA_1.3.1.tgz(r-4.6-any)CSOA_1.3.1.tgz(r-4.5-any)
CSOA_1.3.1.tar.gz(r-4.7-any)CSOA_1.3.1.tar.gz(r-4.6-any)
CSOA_1.3.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
CSOA/json (API)
NEWS

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

Bug tracker:https://github.com/andrei-stoica26/csoa/issues

On BioConductor:CSOA-1.3.0(bioc 3.24)CSOA-1.2.0(bioc 3.23)

softwaresinglecellgenesetenrichmentgeneexpression

5.86 score 1 packages 5 scripts 178 downloads 20 exports 180 dependencies

Last updated from:959ac2950f. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE258
linux-devel-x86_64OK451
source / vignettesOK443
linux-release-x86_64OK539
macos-release-arm64OK348
macos-oldrel-arm64OK334
windows-develOK1479
windows-releaseOK1788
windows-oldrelOK1313
wasm-releaseOK247

Exports:attachCellScoresbasicHeatmapbreakWeakTiescellDistributioncellSetsOverlapsexpMatfeatureWesgeneRadialPlotgenerateOverlapsgetPairsoverlapCutoffPlotoverlapGenesoverlapNetworkPlotoverlapPairspercentileSetsprocessOverlapsqGrabrunCSOAscoreCellsscoreModules

Dependencies:abdivabindapeaskpassbase64encBHBiobaseBiocGenericsbitopsbslibcachemcaToolsclasscliclustercodetoolscommonmarkcowplotcpp11crosstalkcurldata.tableDelayedArraydeldirdigestdotCall64dplyrdqrngevaluatefarverfastDummiesfastmapfitdistrplusFNNfontawesomefsfuturefuture.applygenericsGenomicRangesggalluvialggeasyggforceggnewscaleggplot2ggraphggrepelggridgesglobalsgluegoftestgplotsgraphlayoutsgridExtragtablegtoolshennaherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphIRangesirlbaisobandjquerylibjsonlitekernlabKernSmoothkerntoolsknitrlabelinglaterlatticelazyevallifecyclelistenvliverlmtestmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeminiUInlmeopensslotelpaletteerparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprismaticprogressrpromisespurrrqs2R6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppParallelRcppProgressRcppTOMLrematch2reshape2reticulaterlangrmarkdownROCRrprojrootRSpectrarstudioapiRtsneS4ArraysS4VectorsS7sassscalesscattermoresctransformSeqinfoSeuratSeuratObjectshinysitmoslamsourcetoolsspspamSparseArrayspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringfishstringistringrSummarizedExperimentsurvivalsyssystemfontstensortextshapetibbletidygraphtidyrtidyselecttinytextweenrutf8uwotvctrsviridisviridisLitewithrxfunxtableXVectoryamlzoo

Advanced CSOA

Andrei-Florian Stoica

Rendered fromAdvanced-CSOA.Rmdusingknitr::rmarkdownon May 06 2026.

Last update: 2026-03-11
Started: 2025-08-13

CSOA

Andrei-Florian Stoica

Rendered fromCSOA.Rmdusingknitr::rmarkdownon May 06 2026.

Last update: 2025-10-22
Started: 2025-06-06

The CSOA algorithm

Andrei-Florian Stoica

Rendered fromThe-CSOA-algorithm.Rmdusingknitr::rmarkdownon May 06 2026.

Last update: 2026-04-17
Started: 2025-08-13