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 205 dependencies

Last updated 1 months agofrom:b316159956. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 02 2024
R-4.5-winNOTEDec 02 2024
R-4.5-linuxNOTEDec 02 2024
R-4.4-winNOTEDec 02 2024
R-4.4-macNOTEDec 02 2024
R-4.3-winOKDec 02 2024
R-4.3-macOKDec 02 2024

Exports:addCoordinatescreateSCEcreateSeuratcreateVisiumSCEmarkClusterColparseImageremoveSpotsrunShinySpanielselectSpotsspanielPlot

Dependencies:abindaskpassassortheadbase64encbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularbitopsblusterbslibcachemCairocaToolscliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDelayedArrayDelayedMatrixStatsdeldirdigestdotCall64dplyrdqrngDropletUtilsedgeRevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomeformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggplot2ggrastrggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsHDF5ArrayherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphIRangesirlbaisobandjpegjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleidenlifecyclelimmalistenvlmtestlocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemetapodmgcvmimeminiUImunsellnlmeopensslparallellypatchworkpbapplypheatmappillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR.methodsS3R.ooR.utilsR6raggRANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppMLRcppProgressRcppTOMLreshape2reticulaterhdf5rhdf5filtersRhdf5librlangrmarkdownROCRrprojrootRSpectrarsvdRtsneS4ArraysS4VectorssassScaledMatrixscalesscaterscattermorescransctransformscuttleSeuratSeuratObjectshinySingleCellExperimentsitmosnowsourcetoolsspspamSparseArraysparseMatrixStatsspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstensortextshapingtibbletidyrtidyselecttinytexUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrxfunxtableXVectoryamlzlibbioczoo

Spaniel 10X Visium

Rachel Queen

Rendered fromspaniel-vignette-tenX-import.Rmdusingknitr::rmarkdownon Dec 02 2024.

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