This package is considered a duplicate. The official version of this package is found at:https://bioc.r-universe.dev/VisiumIO

Package: VisiumIO 1.9.5

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_1.9.5.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_1.9.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
VisiumIO/json (API)

# Install 'VisiumIO' in R:

install.packages('VisiumIO', repos = c('https://link-ny.r-universe.dev', 'https://cloud.r-project.org'))

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

On BioConductor:VisiumIO-1.9.5(bioc 3.24)VisiumIO-1.8.0(bioc 3.23)

software infrastructure dataimport singlecell spatial bioconductor-package genomics u24ca289073

6.89 score 3 stars 1 packages 109 scripts 12 exports 90 dependencies

Last updated from:3380deea05. Checks:9 OK. Indexed: no.

Target	Result	Time
linux-devel-x86_64	OK	294
source / vignettes	OK	278
linux-release-x86_64	OK	273
macos-release-arm64	OK	175
macos-oldrel-arm64	OK	199
windows-devel	OK	251
windows-release	OK	237
windows-oldrel	OK	220
wasm-release	OK	155

Exports:compareBarcodes import st_invert_y TENxGeoJSON TENxMappingParquet TENxParquet TENxSpatialCSV TENxSpatialList TENxSpatialParquet TENxVisium TENxVisiumHD TENxVisiumList

Dependencies:abind askpass Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake bit bit64 blob cachem class classInt cli clipr cpp11 crayon curl DBI dbplyr DelayedArray dir.expiry dplyr e1071 fastmap filelock generics GenomicRanges glue h5mread HDF5Array hms httr2 IRanges jsonlite KernSmooth lattice lifecycle magick magrittr MASS Matrix MatrixGenerics matrixStats memoise openssl pillar pkgconfig prettyunits progress proxy purrr R.methodsS3 R.oo R.utils R6 rappdirs Rcpp readr rhdf5 rhdf5filters Rhdf5lib rjson rlang RSQLite s2 S4Arrays S4Vectors Seqinfo sf SingleCellExperiment SparseArray SpatialExperiment stringi stringr SummarizedExperiment sys TENxIO tibble tidyr tidyselect tzdb units utf8 vctrs vroom withr wk XVector

VisiumIO: Import 10X Genomics Visium Experiment Data

Rendered fromVisiumIO.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Compare barcodes between raw and filtered data	compareBarcodes
Flip the Y-axis of cell or nucleus segmentations to align with H&E image	st_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