Package: stJoincount 1.7.0
Jiarong Song
stJoincount: stJoincount - Join count statistic for quantifying spatial correlation between clusters
stJoincount facilitates the application of join count analysis to spatial transcriptomic data generated from the 10x Genomics Visium platform. This tool first converts a labeled spatial tissue map into a raster object, in which each spatial feature is represented by a pixel coded by label assignment. This process includes automatic calculation of optimal raster resolution and extent for the sample. A neighbors list is then created from the rasterized sample, in which adjacent and diagonal neighbors for each pixel are identified. After adding binary spatial weights to the neighbors list, a multi-categorical join count analysis is performed to tabulate "joins" between all possible combinations of label pairs. The function returns the observed join counts, the expected count under conditions of spatial randomness, and the variance calculated under non-free sampling. The z-score is then calculated as the difference between observed and expected counts, divided by the square root of the variance.
Authors:
stJoincount_1.7.0.tar.gz
stJoincount_1.7.0.zip(r-4.5)stJoincount_1.7.0.zip(r-4.4)stJoincount_1.7.0.zip(r-4.3)
stJoincount_1.7.0.tgz(r-4.4-any)stJoincount_1.7.0.tgz(r-4.3-any)
stJoincount_1.7.0.tar.gz(r-4.5-noble)stJoincount_1.7.0.tar.gz(r-4.4-noble)
stJoincount_1.7.0.tgz(r-4.4-emscripten)
stJoincount.pdf |stJoincount.html✨
stJoincount/json (API)
NEWS
| # Install 'stJoincount' in R: |
| install.packages('stJoincount', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/nina-song/stjoincount/issues
On BioConductor:stJoincount-1.7.0(bioc 3.20)stJoincount-1.6.0(bioc 3.19)
Last updated 2 months agofrom:1b562c60c3
Exports:customDictdataPrepFromSeuratdataPrepFromSpEextentBufferjoincountAnalysismosaicIntPlotrasterizeEachClusterrasterPrepresolutionCalczscoreMatrixzscorePlot
Dependencies:abindaskpassbase64encBHBiobaseBiocFileCacheBiocGenericsbitbit64bitopsblobbootbslibcachemcaToolsclassclassIntcliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydeldirdigestdotCall64dplyrdqrnge1071evaluatefansifarverfastDummiesfastmapfilelockfitdistrplusFNNfontawesomefsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphIRangesirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleidenlifecyclelistenvlmtestmagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslparallellypatchworkpbapplypheatmappillarpkgconfigplogrplotlyplyrpngpolyclipprogressrpromisesproxypurrrR6RANNrappdirsrasterRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulaterjsonrlangrmarkdownROCRrprojrootRSpectraRSQLiteRtsnes2S4ArraysS4VectorssassscalesscattermoresctransformSeuratSeuratObjectsfshinySingleCellExperimentsitmosourcetoolsspspamSparseArraySpatialExperimentspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.utilsspDataspdepstringistringrSummarizedExperimentsurvivalsystensorterratibbletidyrtidyselecttinytexUCSC.utilsunitsutf8uwotvctrsviridisLitewithrwkxfunxtableXVectoryamlzlibbioczoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Generate dict of cluster names | customDict |
| Data Preparation from Seurat Object | dataPrepFromSeurat |
| Data Preparation from SpatialExperiment Object | dataPrepFromSpE |
| Find optimal number of buffer for extent | extentBuffer |
| Join count analysis | joincountAnalysis |
| Mosaic plot | mosaicIntPlot |
| Create a raster object from a labeled sample | rasterizeEachCluster |
| Raster layer preparation | rasterPrep |
| Resolution calculation | resolutionCalc |
| Generate Z-score matrix | zscoreMatrix |
| Visulization of Z-score heatmap. | zscorePlot |
