Package: Spaniel 1.21.0

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:Rachel Queen [aut, cre]

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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'))

Peer review:

On BioConductor:Spaniel-1.21.0(bioc 3.21)Spaniel-1.20.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

singlecellrnaseqqualitycontrolpreprocessingnormalizationvisualizationtranscriptomicsgeneexpressionsequencingsoftwaredataimportdatarepresentationinfrastructurecoverageclustering

4.34 score 22 scripts 174 downloads 10 exports 204 dependencies

Last updated 3 months agofrom:b316159956. Checks:3 OK, 4 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 01 2025
R-4.5-winNOTEJan 01 2025
R-4.5-linuxNOTEJan 01 2025
R-4.4-winNOTEJan 01 2025
R-4.4-macNOTEJan 01 2025
R-4.3-winOKJan 01 2025
R-4.3-macOKJan 01 2025

Exports:addCoordinatescreateSCEcreateSeuratcreateVisiumSCEmarkClusterColparseImageremoveSpotsrunShinySpanielselectSpotsspanielPlot

Dependencies:abindaskpassassortheadbase64encbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularbitopsblusterbslibcachemCairocaToolscliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDelayedArrayDelayedMatrixStatsdeldirdigestdotCall64dplyrdqrngDropletUtilsedgeRevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomeformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggplot2ggrastrggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsHDF5ArrayherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphIRangesirlbaisobandjpegjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleidenlifecyclelimmalistenvlmtestlocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemetapodmgcvmimeminiUImunsellnlmeopensslparallellypatchworkpbapplypheatmappillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR.methodsS3R.ooR.utilsR6raggRANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppMLRcppProgressRcppTOMLreshape2reticulaterhdf5rhdf5filtersRhdf5librlangrmarkdownROCRrprojrootRSpectrarsvdRtsneS4ArraysS4VectorssassScaledMatrixscalesscaterscattermorescransctransformscuttleSeuratSeuratObjectshinySingleCellExperimentsitmosnowsourcetoolsspspamSparseArraysparseMatrixStatsspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstensortextshapingtibbletidyrtidyselecttinytexUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrxfunxtableXVectoryamlzoo

Spaniel 10X Visium

Rachel Queen

Rendered fromspaniel-vignette-tenX-import.Rmdusingknitr::rmarkdownon Jan 01 2025.

Last update: 2021-05-13
Started: 2021-05-11