Package: Statial 1.9.0

Farhan Ameen

Statial: A package to identify changes in cell state relative to spatial associations

Statial is a suite of functions for identifying changes in cell state. The functionality provided by Statial provides robust quantification of cell type localisation which are invariant to changes in tissue structure. In addition to this Statial uncovers changes in marker expression associated with varying levels of localisation. These features can be used to explore how the structure and function of different cell types may be altered by the agents they are surrounded with.

Authors:Farhan Ameen [aut, cre], Sourish Iyengar [aut], Shila Ghazanfar [aut], Ellis Patrick [aut]

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Statial.pdf |Statial.html✨
Statial/json (API)

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

Bug tracker:https://github.com/sydneybiox/statial/issues

Pkgdown site:https://sydneybiox.github.io

Datasets:

On BioConductor:Statial-1.9.0(bioc 3.21)Statial-1.8.0(bioc 3.20)

singlecellspatialclassificationsingle-cell

6.49 score 5 stars 23 scripts 212 downloads 16 exports 216 dependencies

Last updated 5 months agofrom:b4c031f4af. Checks:1 OK, 6 ERROR, 2 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 18 2025
R-4.5-winERRORMar 20 2025
R-4.5-macWARNINGMar 18 2025
R-4.5-linuxERRORMar 18 2025
R-4.4-winERRORMar 20 2025
R-4.4-macWARNINGMar 20 2025
R-4.4-linuxERRORMar 20 2025
R-4.3-winERRORMar 20 2025
R-4.3-macERRORMar 20 2025

Exports:calcContaminationcalcStateChangesgetAbundancesgetDistancesgetMarkerMeansgetParentPhyloisKontextualkontextCurvekontextPlotKontextualmakeWindowparentCombinationsplotStateChangesprepMatrixrelabelrelabelKontextual

Dependencies:abindALLapeaplotaskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocParallelbitbit64blobbootbroombslibcachemcarcarDatacirclizeclassclassIntcliclueclustercodetoolscolorRampscolorspaceComplexHeatmapconcavemanConsensusClusterPluscorrplotcowplotcpp11crayoncrosstalkcurlcytolibdata.tableDBIdbplyrDelayedArraydeldirDerivdiffcytdigestdoBydoParalleldplyre1071edgeRevaluatefansifarverfastmapfilelockflowCoreFlowSOMfontawesomeforeachformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggforceggfunggiraphggnewscaleggplot2ggplotifyggpubrggrepelggsciggsignifggtreeGlobalOptionsgluegoftestgridExtragridGraphicsgtablehighrhopachhtmltoolshtmlwidgetshttrigraphIRangesisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalme4locfitmagickmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrmultcompmunsellmvtnormnlmenloptrnnetnumDerivopensslpatchworkpbkrtestpillarpkgconfigplogrplotlyplyrpngpolyclippolynompromisesproxypurrrquantregR6rangerrappdirsrbibutilsRColorBrewerRcppRcppEigenRdpackreformulasreshape2Rhdf5librjsonrlangrmarkdownRProtoBufLibRSQLiterstatixRtsnes2S4ArraysS4VectorssandwichsassscalessfshapeSingleCellExperimentsnowSparseArraySparseMSpatialExperimentspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstensorTH.datatibbletidyrtidyselecttidytreetinytextreeiotreekoRtweenrUCSC.utilsunitsutf8uuidV8vctrsviridisLitewithrwkxfunXMLXVectoryamlyulab.utilszoo

Statial

Farhan Ameen, Sourish Iyengar, Alex Qin, Ellis Patrick

Rendered fromStatial.Rmdusingknitr::rmarkdownon Mar 18 2025.

Last update: 2024-10-23
Started: 2022-09-18