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Bioconductor - SpatialExperimentIO (development version)

SpatialExperimentIO

This is the development version of SpatialExperimentIO; for the stable release version, see SpatialExperimentIO.

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

Bioconductor version: Development (3.22)

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.

Author: Yixing E. Dong [aut, cre] ORCID: 0009-0003-5115-5686

Maintainer: Yixing E. Dong <estelladong729 at gmail.com>

Citation (from within R, enter citation("SpatialExperimentIO")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("SpatialExperimentIO")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SpatialExperimentIO")
Details biocViews DataImport, DataRepresentation, GeneExpression, Infrastructure, SingleCell, Software, Spatial, Transcriptomics Version 1.1.0 In Bioconductor since BioC 3.21 (R-4.5) (< 6 months) License Artistic-2.0 Depends R (>= 4.1.0) Imports DropletUtils, SpatialExperiment, SingleCellExperiment, methods, data.table, arrow, purrr, S4Vectors System Requirements URL https://github.com/estellad/SpatialExperimentIO Bug Reports https://github.com/estellad/SpatialExperimentIO/issues See More Package Archives

Follow Installation instructions to use this package in your R session.


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