Package: spatialDE 1.19.0

Gabriele Sales

spatialDE: R wrapper for SpatialDE

SpatialDE is a method to find spatially variable genes (SVG) from spatial transcriptomics data. This package provides wrappers to use the Python SpatialDE library in R, using reticulate and basilisk.

Authors:Davide Corso [aut], Milan Malfait [aut], Lambda Moses [aut], Gabriele Sales [cre]

spatialDE_1.19.0.tar.gz
spatialDE_1.19.0.zip(r-4.7)spatialDE_1.19.0.zip(r-4.6)spatialDE_1.19.0.zip(r-4.5)
spatialDE_1.19.0.tgz(r-4.6-any)spatialDE_1.19.0.tgz(r-4.5-any)
spatialDE_1.19.0.tar.gz(r-4.7-any)spatialDE_1.19.0.tar.gz(r-4.6-any)
spatialDE_1.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
spatialDE/json (API)

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

Bug tracker:https://github.com/sales-lab/spatialde/issues

Datasets:

On BioConductor:spatialDE-1.19.0(bioc 3.24)spatialDE-1.18.0(bioc 3.23)

softwaretranscriptomicspythonspatial-datawrapper

6.76 score 3 stars 160 scripts 344 downloads 2 mentions 11 exports 79 dependencies

Last updated from:59649f3313. Checks:8 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE181
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source / vignettesOK1592
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macos-release-arm64NOTE912
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Exports:FSV_sigmockSVGmodel_searchmodelSearchmultiGenePlotsregress_outrunspatial_patternsspatialDEspatialPatternsstabilize

Dependencies:abindaskpassbackportsbasiliskBiobaseBiocFileCacheBiocGenericsbitbit64blobcachemcheckmateclicpp11curlDBIdbplyrDelayedArraydir.expirydplyrfarverfastmapfilelockgenericsGenomicRangesggplot2ggrepelgluegridExtragtableherehttr2IRangesisobandjsonlitelabelinglatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoiseopensslpillarpkgconfigpngpurrrR6rappdirsRColorBrewerRcppRcppTOMLreticulaterjsonrlangrprojrootRSQLiteS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrsviridisLitewithrXVector

Introduction to spatialDE

Davide Corso, Milan Malfait, Lambda Moses

Rendered fromspatialDE.Rmdusingknitr::rmarkdownon Jun 11 2026.

Last update: 2021-08-26
Started: 2021-02-14

Readme and manuals

Help Manual

Help pageTopics
Plot Fraction Spatial Variance vs Q-valueFSV_sig
Mouse Olfactory Bulb sample metadataMOB_sample_info
Generate count matrix for spatially variable genes.mockSVG
Compare model fits with different modelsmodel_search
Classify Spatially Variable Genes to interpretable fitting classesmodelSearch modelSearch,matrix-method modelSearch,SpatialExperiment-method
Plot Spatial Patterns of Multiple GenesmultiGenePlots multiGenePlots,matrix-method multiGenePlots,SpatialExperiment-method
Regress out library size effectregress_out
Mouse Olfactory Bulb spatial gene expression dataRep11_MOB_0
Perform SpatialDE testrun
Group spatially variable genes into spatial patterns using automatic expression histology (AEH)spatial_patterns
Find spatially variable genes with *SpatialDE*spatialDE spatialDE,matrix-method spatialDE,SpatialExperiment-method
Automatic expression histology in *SpatialDE*spatialPatterns spatialPatterns,matrix-method spatialPatterns,SpatialExperiment-method
Stabilize variance of countsstabilize