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:
spicyR_1.19.3.tar.gz
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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
- diabetesData - Diabetes IMC data in SCE format.
- spicyTest - Results from spicy for diabetesData
On BioConductor:spicyR-1.19.3(bioc 3.21)spicyR-1.18.0(bioc 3.20)
singlecellcellbasedassaysspatial
Last updated 3 months agofrom:1b87dce47c. Checks:1 OK, 6 NOTE, 1 ERROR. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 18 2025 |
| R-4.5-win | NOTE | Feb 18 2025 |
| R-4.5-mac | NOTE | Feb 18 2025 |
| R-4.5-linux | NOTE | Feb 18 2025 |
| R-4.4-win | NOTE | Feb 18 2025 |
| R-4.4-mac | NOTE | Feb 18 2025 |
| R-4.3-win | NOTE | Feb 18 2025 |
| R-4.3-mac | ERROR | Feb 18 2025 |
Exports:bindcolTestconvPairsgetPairwisegetPropsignifPlotspicyspicyBoxPlottopPairs
Dependencies:abindannotateAnnotationDbiaskpassbackportsbase64encbdsmatrixbeeswarmBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocParallelBiostringsbitbit64bitopsblobbootbroombslibcachemcarcarDatacirclizeclassClassifyRclassIntclicodetoolscolorspacecommonmarkconcavemancorrplotcowplotcoxmecpp11crayoncurlcytomapperdata.tableDBIdbplyrdcanrDelayedArraydeldirDerivdigestdoBydoRNGdplyre1071EBImageevaluatefansifarverfastmapfftwtoolsfilelockfontawesomeforeachformatRFormulafsfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggforceggh4xggnewscaleggplot2ggpubrggrepelggsciggsignifggthemesggupsetGlobalOptionsgluegoftestgridExtragtableh5mreadHDF5ArrayhighrhtmltoolshtmlwidgetshttpuvhttrigraphIRangesisobanditeratorsjpegjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelifecyclelme4lmerTestlocfitmagickmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrMultiAssayExperimentmunsellnlmenloptrnnetnnlsnumDerivopensslpbkrtestpheatmappillarpkgconfigplogrplyrpngpolyclippolynompromisesproxypurrrquantregR6rangerrappdirsrasterrbibutilsRColorBrewerRcppRcppEigenRCurlRdpackreformulasreshape2rhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownrngtoolsRSQLiterstatixs2S4ArraysS4VectorssassscalesscamsfshapeshinyshinydashboardsimpleSegSingleCellExperimentsnowsourcetoolsspSparseArraySparseMSpatialExperimentspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrSummarizedExperimentsurvivalsvglitesvgPanZoomsyssystemfontstensorterratibbletidyrtidyselecttifftinytextweenrUCSC.utilsunitsutf8V8vctrsviporviridisviridisLitewithrwkxfunXMLxtableXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Produces a dataframe showing L-function metric for each imageID entry. | bind |
| Perform a simple wilcoxon-rank-sum test or t-test on the columns of a data frame | colTest |
| Converts colPairs object into an abundance matrix based on number of nearby interactions for every cell type. | convPairs |
| Diabetes IMC data in SCE format. | diabetesData |
| Get statistic from pairwise L curve of a single image. | getPairwise |
| Get proportions from a SummarizedExperiment. | getProp |
| Plots result of signifPlot. | signifPlot |
| Plots boxplot for a specified cell-cell relationship | spicyBoxPlot |
| Performs spatial tests on spatial cytometry data. | spicy spicy,spicy-method SpicyResults,list,ANY-method SpicyResults-class |
| Results from spicy for diabetesData | spicyTest |
| Plots survival results from spicy. | survBubble |
| A table of the significant results from spicy tests | topPairs topPairs,SpicyResults-method |
