Installation | Overview | Example data | Linear modelling | Test for change in localisation for a specific pair of cells | Test for change in localisation for all pairwise cell combinations | Linear modelling for custom metrics | Performing survival analysis | Accounting for tissue inhomogeneity | Mixed effects modelling | References
Package: spicyR 1.25.0
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_1.25.0.tar.gz
spicyR_1.25.0.zip(r-4.7)spicyR_1.25.0.zip(r-4.6)spicyR_1.25.0.zip(r-4.5)
spicyR_1.25.0.tgz(r-4.6-any)spicyR_1.25.0.tgz(r-4.5-any)
spicyR_1.25.0.tar.gz(r-4.7-any)spicyR_1.25.0.tar.gz(r-4.6-any)
spicyR_1.25.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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/docs site:https://sydneybiox.github.io
Datasets:
- diabetesData - Diabetes IMC data in SCE format.
- spicyTest - Results from spicy for diabetesData
On BioConductor:spicyR-1.25.0(bioc 3.24)spicyR-1.24.0(bioc 3.23)
singlecellcellbasedassaysspatial
Last updated from:3effcf4af6. Checks:1 WARNING, 6 NOTE, 2 OK, 1 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 276 | ||
| linux-devel-x86_64 | NOTE | 514 | ||
| source / vignettes | OK | 581 | ||
| linux-release-x86_64 | NOTE | 511 | ||
| macos-release-arm64 | FAIL | 101 | ||
| macos-oldrel-arm64 | NOTE | 220 | ||
| windows-devel | NOTE | 439 | ||
| windows-release | NOTE | 429 | ||
| windows-oldrel | NOTE | 428 | ||
| wasm-release | OK | 299 |
Exports:bindcolTestconvPairsgetPairwisegetPropimageCrossPlotplotImagesignifPlotspicyspicyBoxPlottopPairs
Dependencies:abindannotateAnnotationDbiaskpassbackportsbase64encbdsmatrixbeeswarmBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsbiocmakeBiocParallelBiostringsbitbit64bitopsblobbootbroombslibcachemcarcarDatacirclizeclassClassifyRclassIntclicodetoolscolorspacecommonmarkconcavemancorrplotcowplotcoxmecpp11crayoncurlcytomapperdata.tableDBIdbplyrdcanrDelayedArraydeldirDerivdigestdir.expirydoBydoRNGdplyre1071EBImageevaluatefarverfastmapfftwtoolsfilelockfontawesomeforeachforecastformatRFormulafracdifffsfutile.loggerfutile.optionsgenefiltergenericsGenomicRangesggbeeswarmggforceggh4xggnewscaleggplot2ggpubrggrepelggsciggsignifggthemesggupsetGlobalOptionsgluegoftestgridExtragtableh5mreadHDF5Arrayhighrhtmltoolshtmlwidgetshttpuvhttrhttr2igraphIRangesisobanditeratorsjpegjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelifecyclelme4lmerTestlmtestlocfitmagickmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmimeminqamodelrMultiAssayExperimentnlmenloptrnnetnnlsnumDerivopensslotelpbkrtestpheatmappillarpkgconfigplyrpngpolyclippolynompromisesproxypurrrquantregR6rangerrappdirsrasterrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRCurlRdpackreformulasreshape2rhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownrngtoolsRSQLiterstatixs2S4ArraysS4VectorsS7sassscalesscamSeqinfosfshapeshinyshinydashboardsimpleSegSingleCellExperimentsnowsourcetoolsspSparseArraySparseMSpatialExperimentspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrSummarizedExperimentsurvivalsvglitesvgPanZoomsyssystemfontstensorterratextshapingtibbletidyrtidyselecttifftimeDatetinytextweenrunitsurcautf8V8vctrsviporviridisviridisLitewithrwkxfunXMLxtableXVectoryamlzoo
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 |
| Pairwise cross-plot of spatial associations | imageCrossPlot |
| Plots an image with specified from and to cell types. | plotImage |
| 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 |
