Package: sosta 0.99.3

Samuel Gunz

sosta: A package for the analysis of anatomical tissue structures in spatial omics data

`sosta` (Spatial Omics STructure Analysis) is a package for analyzing spatial omics data to explore tissue organization at the anatomical structure level. It reconstructs morphologically relevant structures based on molecular features or cell types. It further calculates a range of structural and shape metrics to quantitatively describe tissue architecture. The package is designed to integrate with other packages for the analysis of spatial (omics) data.

Authors:Samuel Gunz [aut, cre], Mark D. Robinson [aut, fnd]

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sosta.pdf |sosta.html✨
sosta/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/sgunz/sosta/issues

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

On BioConductor:sosta-0.99.3(bioc 3.21)

softwarespatialtranscriptomicsvisualization

4.88 score 1 stars 2 scripts 17 exports 100 dependencies

Last updated 17 days agofrom:225afd3a78. Checks:5 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 20 2025
R-4.5-winOKJan 20 2025
R-4.5-linuxOKJan 20 2025
R-4.4-winOKJan 20 2025
R-4.4-macOKJan 20 2025

Exports:binaryImageToSFestimateReconstructionParametersSPEfindIntensityThresholdgetDimXYmeanShapeMetricsnormalizeCoordinatesreconstructShapeDensityreconstructShapeDensityImagereconstructShapeDensitySPEshapeIntensityImageshapeMetricsSPE2pppst_calculateCurvaturest_calculateShapeCurlst_feature_axestotalShapeMetricsxyCoordinates

Dependencies:abindaskpassBiobaseBiocFileCacheBiocGenericsbitbit64blobcachemclassclassIntclicolorspacecpp11crayoncurlDBIdbplyrDelayedArraydeldirdplyre1071fansifarverfastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegoftestgtablehttrIRangesisobandjsonliteKernSmoothlabelinglatticelifecyclemagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpatchworkpillarpkgconfigplogrpolyclipproxypurrrR6RColorBrewerRcpprjsonrlangRSQLites2S4ArraysS4VectorsscalessfSingleCellExperimentsmoothrSparseArraySpatialExperimentspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrSummarizedExperimentsystensorterratibbletidyrtidyselectUCSC.utilsunitsutf8vctrsviridisLitewithrwkXVector

Reconstruction and analysis of pancreatic islets from IMC data

Samuel Gunz, Mark D. Robinson

Rendered fromIMC_DiabetesIslets_Vignette.Rmdusingknitr::rmarkdownon Jan 20 2025.

Last update: 2025-01-03
Started: 2024-09-26