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✨
DESCRIPTION |NEWS
card.svg |card.png
SpatialExperimentIO/json (API)

# 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)

datarepresentation dataimport infrastructure transcriptomics singlecell spatial geneexpression

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.

Target	Result	Time
bioc-checks	NOTE	193
linux-devel-x86_64	NOTE	397
source / vignettes	OK	650
linux-release-x86_64	NOTE	401
macos-release-arm64	NOTE	323
macos-oldrel-arm64	NOTE	255
windows-devel	NOTE	279
windows-release	NOTE	303
windows-oldrel	NOTE	268
wasm-release	OK	179

Exports:addParquetPathsCosmx addParquetPathsXenium addParquetPathToMeta csvToParquetPaths readCosmxSXE readMerscopeSXE readSeqfishSXE readStarmapplusSXE readXeniumSXE

Dependencies:abind arrow askpass assertthat assorthead beachmat BH Biobase BiocFileCache BiocGenerics biocmake BiocParallel bit bit64 blob cachem cli codetools cpp11 curl data.table DBI dbplyr DelayedArray DelayedMatrixStats dir.expiry dplyr dqrng DropletUtils edgeR fastmap filelock formatR futile.logger futile.options generics GenomicRanges glue h5mread HDF5Array httr2 IRanges lambda.r lattice lifecycle limma locfit magick magrittr Matrix MatrixGenerics matrixStats memoise openssl pillar pkgconfig purrr R.methodsS3 R.oo R.utils R6 rappdirs Rcpp rhdf5 rhdf5filters Rhdf5lib rjson rlang RSQLite S4Arrays S4Vectors scuttle Seqinfo SingleCellExperiment sitmo snow SparseArray sparseMatrixStats SpatialExperiment statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect utf8 vctrs withr XVector

SpatialExperimentIO - Data Reader Package Overview

Rendered fromSpatialExperimentIO.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Sanity check if one and only file with the specified name pattern exists in the data download directory, and return the file path to .csv Used for count matrix and metadata only, as they require unique.	.sanityCheck
Add CosMx-related parquet paths to metadata for transcripts, polygon, or cell/nucleus boundaries.	addParquetPathsCosmx
Add Xenium-related parquet paths to metadata for transcripts or cell/nucleus boundaries.	addParquetPathsXenium
Add parquet paths to metadata for transcripts, polygon, or cell/nucleus boundaries.	addParquetPathToMeta
If transcripts or polygon is expected to be loaded, write a parquet file to the current data download (if not already), and return the file path to .parquet	csvToParquetPaths
Load data from a Nanostring CosMx experiment	readCosmxSXE
Load data from a Vizgen MERSCOPE experiment	readMerscopeSXE
Load data from a Spatial Genomics seqFISH experiment	readSeqfishSXE
Load data from a STARmap PLUS experiment	readStarmapplusSXE
Load data from a 10x Geonomics Xenium experiment	readXeniumSXE