Package: spicyR 1.19.3

Ellis Patrick

spicyR: Spatial analysis of in situ cytometry data

The spicyR package provides a framework for performing inference on changes in spatial relationships between pairs of cell types for cell-resolution spatial omics technologies. spicyR consists of three primary steps: (i) summarizing the degree of spatial localization between pairs of cell types for each image; (ii) modelling the variability in localization summary statistics as a function of cell counts and (iii) testing for changes in spatial localizations associated with a response variable.

Authors:Nicolas Canete [aut], Ellis Patrick [aut, cre], Nicholas Robertson [ctb], Alex Qin [ctb], Farhan Ameen [ctb], Shreya Rao [ctb]

spicyR_1.19.3.tar.gz
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spicyR_1.19.3.tar.gz(r-4.5-noble)spicyR_1.19.3.tar.gz(r-4.4-noble)
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spicyR.pdf |spicyR.html
spicyR/json (API)

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

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

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

Datasets:

On BioConductor:spicyR-1.19.3(bioc 3.21)spicyR-1.18.0(bioc 3.20)

singlecellcellbasedassaysspatial

7.99 score 9 stars 1 packages 57 scripts 392 downloads 9 exports 224 dependencies

Last updated 3 months agofrom:1b87dce47c. Checks:1 OK, 6 NOTE, 1 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 18 2025
R-4.5-winNOTEFeb 18 2025
R-4.5-macNOTEFeb 18 2025
R-4.5-linuxNOTEFeb 18 2025
R-4.4-winNOTEFeb 18 2025
R-4.4-macNOTEFeb 18 2025
R-4.3-winNOTEFeb 18 2025
R-4.3-macERRORFeb 18 2025

Exports:bindcolTestconvPairsgetPairwisegetPropsignifPlotspicyspicyBoxPlottopPairs

Dependencies:abindannotateAnnotationDbiaskpassbackportsbase64encbdsmatrixbeeswarmBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocParallelBiostringsbitbit64bitopsblobbootbroombslibcachemcarcarDatacirclizeclassClassifyRclassIntclicodetoolscolorspacecommonmarkconcavemancorrplotcowplotcoxmecpp11crayoncurlcytomapperdata.tableDBIdbplyrdcanrDelayedArraydeldirDerivdigestdoBydoRNGdplyre1071EBImageevaluatefansifarverfastmapfftwtoolsfilelockfontawesomeforeachformatRFormulafsfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggforceggh4xggnewscaleggplot2ggpubrggrepelggsciggsignifggthemesggupsetGlobalOptionsgluegoftestgridExtragtableh5mreadHDF5ArrayhighrhtmltoolshtmlwidgetshttpuvhttrigraphIRangesisobanditeratorsjpegjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelifecyclelme4lmerTestlocfitmagickmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrMultiAssayExperimentmunsellnlmenloptrnnetnnlsnumDerivopensslpbkrtestpheatmappillarpkgconfigplogrplyrpngpolyclippolynompromisesproxypurrrquantregR6rangerrappdirsrasterrbibutilsRColorBrewerRcppRcppEigenRCurlRdpackreformulasreshape2rhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownrngtoolsRSQLiterstatixs2S4ArraysS4VectorssassscalesscamsfshapeshinyshinydashboardsimpleSegSingleCellExperimentsnowsourcetoolsspSparseArraySparseMSpatialExperimentspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrSummarizedExperimentsurvivalsvglitesvgPanZoomsyssystemfontstensorterratibbletidyrtidyselecttifftinytextweenrUCSC.utilsunitsutf8V8vctrsviporviridisviridisLitewithrwkxfunXMLxtableXVectoryaml

Spatial Linear and Mixed-Effects Modelling with spicyR

Rendered fromspicyR.Rmdusingknitr::rmarkdownon Feb 18 2025.

Last update: 2024-11-13
Started: 2022-11-10