Package: SpatialExperimentIO 1.5.0

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_1.5.0.tar.gz
SpatialExperimentIO_1.5.0.zip(r-4.7)SpatialExperimentIO_1.5.0.zip(r-4.6)SpatialExperimentIO_1.5.0.zip(r-4.5)
SpatialExperimentIO_1.5.0.tgz(r-4.6-any)SpatialExperimentIO_1.5.0.tgz(r-4.5-any)
SpatialExperimentIO_1.5.0.tar.gz(r-4.7-any)SpatialExperimentIO_1.5.0.tar.gz(r-4.6-any)
SpatialExperimentIO_1.5.0.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.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

6.59 score 19 stars 1 packages 69 scripts 296 downloads 9 exports 91 dependencies

Last updated from:56f593fd6d. Checks:8 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE193
linux-devel-x86_64NOTE397
source / vignettesOK650
linux-release-x86_64NOTE401
macos-release-arm64NOTE323
macos-oldrel-arm64NOTE255
windows-develNOTE279
windows-releaseNOTE303
windows-oldrelNOTE268
wasm-releaseOK179

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 08 2026.

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