Package: SpatialExperimentIO 1.4.0

Yixing E. Dong

SpatialExperimentIO: Read in Xenium, CosMx, MERSCOPE or STARmapPLUS data as SpatialExperiment object

Read in imaging-based spatial transcriptomics technology data. Current available modules are for Xenium by 10X Genomics, CosMx by Nanostring, MERSCOPE by Vizgen, or STARmapPLUS from Broad Institute. You can choose to read the data in as a SpatialExperiment or a SingleCellExperiment object.

Authors:Yixing E. Dong [aut, cre]

SpatialExperimentIO_1.4.0.tar.gz
SpatialExperimentIO_1.4.0.zip(r-4.7)SpatialExperimentIO_1.4.0.zip(r-4.6)SpatialExperimentIO_1.4.0.zip(r-4.5)
SpatialExperimentIO_1.4.0.tgz(r-4.6-any)SpatialExperimentIO_1.4.0.tgz(r-4.5-any)
SpatialExperimentIO_1.4.0.tar.gz(r-4.7-any)SpatialExperimentIO_1.4.0.tar.gz(r-4.6-any)
SpatialExperimentIO_1.4.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SpatialExperimentIO/json (API)
NEWS

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

Bug tracker:https://github.com/estellad/spatialexperimentio/issues

On BioConductor:SpatialExperimentIO-1.5.0(bioc 3.24)SpatialExperimentIO-1.4.0(bioc 3.23)

datarepresentationdataimportinfrastructuretranscriptomicssinglecellspatialgeneexpression

6.61 score 19 stars 1 packages 71 scripts 9 exports 91 dependencies

Last updated from:4cd6a8b74f (on RELEASE_3_23). Checks:8 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE191
linux-devel-x86_64NOTE367
source / vignettesOK268
linux-release-x86_64NOTE369
macos-release-arm64NOTE216
macos-oldrel-arm64NOTE206
windows-develNOTE298
windows-releaseNOTE284
windows-oldrelNOTE252
wasm-releaseOK167

Exports:addParquetPathsCosmxaddParquetPathsXeniumaddParquetPathToMetacsvToParquetPathsreadCosmxSXEreadMerscopeSXEreadSeqfishSXEreadStarmapplusSXEreadXeniumSXE

Dependencies:abindarrowaskpassassertthatassortheadbeachmatBHBiobaseBiocFileCacheBiocGenericsbiocmakeBiocParallelbitbit64blobcachemclicodetoolscpp11curldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdir.expirydplyrdqrngDropletUtilsedgeRfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicRangesglueh5mreadHDF5Arrayhttr2IRangeslambda.rlatticelifecyclelimmalocfitmagickmagrittrMatrixMatrixGenericsmatrixStatsmemoiseopensslpillarpkgconfigpurrrR.methodsS3R.ooR.utilsR6rappdirsRcpprhdf5rhdf5filtersRhdf5librjsonrlangRSQLiteS4ArraysS4VectorsscuttleSeqinfoSingleCellExperimentsitmosnowSparseArraysparseMatrixStatsSpatialExperimentstatmodstringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrswithrXVector

SpatialExperimentIO - Data Reader Package Overview

Yixing E. Dong

Rendered fromSpatialExperimentIO.Rmdusingknitr::rmarkdownon Jun 18 2026.

Last update: 2025-02-03
Started: 2023-11-20