Package: spatialDE 1.13.0

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_1.13.0.tar.gz
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spatialDE.pdf |spatialDE.html✨
spatialDE/json (API)

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

Peer review:

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

Datasets:

On BioConductor:spatialDE-1.13.0(bioc 3.21)spatialDE-1.12.0(bioc 3.20)

softwaretranscriptomicspythonspatial-datawrapper

5.96 score 3 stars 17 scripts 204 downloads 2 mentions 11 exports 91 dependencies

Last updated 25 days agofrom:03b4e0efd8. Checks:OK: 1 NOTE: 3 WARNING: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winWARNINGOct 31 2024
R-4.5-linuxNOTEOct 31 2024
R-4.4-winWARNINGOct 31 2024
R-4.4-macNOTEOct 31 2024
R-4.3-winWARNINGOct 31 2024
R-4.3-macNOTEOct 31 2024

Exports:FSV_sigmockSVGmodel_searchmodelSearchmultiGenePlotsregress_outrunspatial_patternsspatialDEspatialPatternsstabilize

Dependencies:abindaskpassbackportsbasiliskbasilisk.utilsBiobaseBiocFileCacheBiocGenericsbitbit64blobcachemcheckmateclicolorspacecpp11crayoncurlDBIdbplyrDelayedArraydir.expirydplyrfansifarverfastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelgluegridExtragtableherehttrIRangesisobandjsonlitelabelinglatticelifecyclemagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngpurrrR6rappdirsRColorBrewerRcppRcppTOMLreticulaterjsonrlangrprojrootRSQLiteS4ArraysS4VectorsscalesSingleCellExperimentSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

Introduction to spatialDE

Davide Corso, Milan Malfait, Lambda Moses

Rendered fromspatialDE.Rmdusingknitr::rmarkdownon Oct 31 2024.

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