Package: Spaniel 1.19.0
Rachel Queen
Spaniel: Spatial Transcriptomics Analysis
Spaniel includes a series of tools to aid the quality control and analysis of Spatial Transcriptomics data. Spaniel can import data from either the original Spatial Transcriptomics system or 10X Visium technology. The package contains functions to create a SingleCellExperiment Seurat object and provides a method of loading a histologial image into R. The spanielPlot function allows visualisation of metrics contained within the S4 object overlaid onto the image of the tissue.
Authors:
Spaniel_1.19.0.tar.gz
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Spaniel_1.19.0.tgz(r-4.4-any)Spaniel_1.19.0.tgz(r-4.3-any)
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Spaniel.pdf |Spaniel.html✨
Spaniel/json (API)
NEWS
| # Install 'Spaniel' in R: |
| install.packages('Spaniel', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:Spaniel-1.19.0(bioc 3.20)Spaniel-1.18.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:c27a0c1a68
Exports:addCoordinatescreateSCEcreateSeuratcreateVisiumSCEmarkClusterColparseImageremoveSpotsrunShinySpanielselectSpotsspanielPlot
Dependencies:abindaskpassbase64encbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularbitopsblusterbslibcachemCairocaToolscliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDelayedArrayDelayedMatrixStatsdeldirdigestdotCall64dplyrdqrngDropletUtilsedgeRevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomeformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggplot2ggrastrggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsHDF5ArrayherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphIRangesirlbaisobandjpegjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleidenlifecyclelimmalistenvlmtestlocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemetapodmgcvmimeminiUImunsellnlmeopensslparallellypatchworkpbapplypheatmappillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR.methodsS3R.ooR.utilsR6raggRANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppMLRcppProgressRcppTOMLreshape2reticulaterhdf5rhdf5filtersRhdf5librlangrmarkdownROCRrprojrootRSpectrarsvdRtsneS4ArraysS4VectorssassScaledMatrixscalesscaterscattermorescransctransformscuttleSeuratSeuratObjectshinySingleCellExperimentsitmosnowsourcetoolsspspamSparseArraysparseMatrixStatsspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.utilsstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstensortextshapingtibbletidyrtidyselecttinytexUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrxfunxtableXVectoryamlzlibbioczoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add coordinates to Object Adds output of Spot Detector coordinates to Seurat object or SCE object created by createSeurat/createSCE. Details about how to use Spot Detector can be found: https://github.com/SpatialTranscriptomicsResearch/st_spot_detector | addCoordinates |
| Create a SingleCellExperiment Object From Spatial Transcriptomics Data | createSCE |
| Create a Seurat Object From Spatial Transcriptomics Data | createSeurat |
| createVisiumSCE | createVisiumSCE |
| markClusterCol | markClusterCol |
| This function parses a HE image to use as the background for plots | parseImage |
| removeSpots | removeSpots |
| RunShinySpaniel | runShinySpaniel |
| selectSpots | selectSpots |
| Spatial Transcriptomics Plot | spanielPlot |
