Package: VisiumIO 1.9.2

Marcel Ramos

VisiumIO: Import Visium data from the 10X Space Ranger pipeline

The package allows users to readily import spatial data obtained from either the 10X website or from the Space Ranger pipeline. Supported formats include tar.gz, h5, and mtx files. Multiple files can be imported at once with *List type of functions. The package represents data mainly as SpatialExperiment objects.

Authors:Marcel Ramos [aut, cre], Estella YiXing Dong [aut, ctb], Dario Righelli [aut, ctb], Helena Crowell [aut, ctb], NCI [fnd]

VisiumIO_1.9.2.tar.gz
VisiumIO_1.9.5.zip(r-4.7)VisiumIO_1.9.5.zip(r-4.6)VisiumIO_1.9.5.zip(r-4.5)
VisiumIO_1.9.5.tgz(r-4.6-any)VisiumIO_1.9.5.tgz(r-4.5-any)
VisiumIO_1.9.5.tar.gz(r-4.7-any)VisiumIO_1.9.5.tar.gz(r-4.6-any)
VisiumIO_1.9.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
VisiumIO/json (API)
NEWS

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

Bug tracker:https://github.com/waldronlab/visiumio/issues

On BioConductor:VisiumIO-1.9.0(bioc 3.24)VisiumIO-1.8.0(bioc 3.23)

softwareinfrastructuredataimportsinglecellspatialbioconductor-packagegenomicsu24ca289073

6.84 score 3 stars 1 packages 95 scripts 12 exports 90 dependencies

Last updated from:f12a653358. Checks:9 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK276
source / vignettesOK251
linux-release-x86_64OK299
macos-release-arm64OK232
macos-oldrel-arm64OK180
windows-develOK669
windows-releaseOK430
windows-oldrelOK235
wasm-releaseOK156

Exports:compareBarcodesimportst_invert_yTENxGeoJSONTENxMappingParquetTENxParquetTENxSpatialCSVTENxSpatialListTENxSpatialParquetTENxVisiumTENxVisiumHDTENxVisiumList

Dependencies:abindaskpassBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObiocmakebitbit64blobcachemclassclassIntclicliprcpp11crayoncurlDBIdbplyrDelayedArraydir.expirydplyre1071fastmapfilelockgenericsGenomicRangesglueh5mreadHDF5Arrayhmshttr2IRangesjsonliteKernSmoothlatticelifecyclemagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoiseopensslpillarpkgconfigprettyunitsprogressproxypurrrR.methodsS3R.ooR.utilsR6rappdirsRcppreadrrhdf5rhdf5filtersRhdf5librjsonrlangRSQLites2S4ArraysS4VectorsSeqinfosfSingleCellExperimentSparseArraySpatialExperimentstringistringrSummarizedExperimentsysTENxIOtibbletidyrtidyselecttzdbunitsutf8vctrsvroomwithrwkXVector

VisiumIO: Import 10X Genomics Visium Experiment Data

Marcel Ramos

Rendered fromVisiumIO.Rmdusingknitr::rmarkdownon May 06 2026.

Last update: 2025-10-14
Started: 2023-11-20

Readme and manuals

Help Manual

Help pageTopics
Compare barcodes between raw and filtered datacompareBarcodes
Flip the Y-axis of cell or nucleus segmentations to align with H&E imagest_invert_y
Import 10X Genomics GeoJSON files.TENxGeoJSON import,TENxGeoJSON,ANY,ANY-method TENxGeoJSON TENxGeoJSON-class
Represent and import Parquet data from 10X Genomics.TENxMappingParquet .TENxParquet import,TENxMappingParquet,ANY,ANY-method TENxMappingParquet TENxMappingParquet-class TENxParquet TENxParquet-class
Represent and import spatial CSV data from 10X Genomics.TENxSpatialCSV import,TENxSpatialCSV,ANY,ANY-method TENxSpatialCSV TENxSpatialCSV-class
A class to represent and import spatial Visium data.TENxSpatialList import,TENxSpatialList,ANY,ANY-method TENxSpatialList TENxSpatialList-class
Represent and import spatial Parquet data from 10X Genomics.TENxSpatialParquet import,TENxSpatialParquet,ANY,ANY-method TENxSpatialParquet TENxSpatialParquet-class
A class to represent and import a single Visium Sample.TENxVisium import,TENxVisium,ANY,ANY-method TENxVisium TENxVisium-class
A class to represent and import multiple Visium HD samples.TENxVisiumHD import,TENxVisiumHD,ANY,ANY-method TENxVisiumHD TENxVisiumHD-class
A class to represent and import multiple Visium samples.TENxVisiumList import,TENxVisiumList,ANY,ANY-method TENxVisiumList TENxVisiumList-class