Package: SpatialExperimentIO 0.99.8

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_0.99.8.tar.gz
SpatialExperimentIO_0.99.8.zip(r-4.5)SpatialExperimentIO_0.99.8.zip(r-4.4)SpatialExperimentIO_0.99.8.zip(r-4.3)
SpatialExperimentIO_0.99.7.tgz(r-4.5-any)SpatialExperimentIO_0.99.8.tgz(r-4.4-any)
SpatialExperimentIO_0.99.8.tar.gz(r-4.5-noble)SpatialExperimentIO_0.99.8.tar.gz(r-4.4-noble)
SpatialExperimentIO_0.99.8.tgz(r-4.4-emscripten)
SpatialExperimentIO.pdf |SpatialExperimentIO.html✨
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-0.99.7(bioc 3.21)

datarepresentationdataimportinfrastructuretranscriptomicssinglecellspatialgeneexpression

5.76 score 8 stars 16 scripts 40 downloads 9 exports 95 dependencies

Last updated 26 days agofrom:6daa4631ea. Checks:1 OK, 1 FAILURE, 5 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 13 2025
R-4.5-winNOTEFeb 13 2025
R-4.5-macOUTDATEDFeb 05 2025
R-4.5-linuxNOTEFeb 13 2025
R-4.4-winNOTEFeb 13 2025
R-4.4-macNOTEFeb 13 2025
R-4.3-winNOTEFeb 13 2025

Exports:addParquetPathsCosmxaddParquetPathsXeniumaddParquetPathToMetacsvToParquetPathsreadCosmxSXEreadMerscopeSXEreadSeqfishSXEreadStarmapplusSXEreadXeniumSXE

Dependencies:abindarrowaskpassassertthatassortheadbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocParallelbitbit64blobcachemclicodetoolscpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdplyrdqrngDropletUtilsedgeRfansifastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesglueh5mreadHDF5ArrayhttrIRangesjsonlitelambda.rlatticelifecyclelimmalocfitmagickmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplogrpurrrR.methodsS3R.ooR.utilsR6Rcpprhdf5rhdf5filtersRhdf5librjsonrlangRSQLiteS4ArraysS4VectorsscuttleSingleCellExperimentsitmosnowSparseArraysparseMatrixStatsSpatialExperimentstatmodstringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXVector

SpatialExperimentIO - Data Reader Package Overview

Yixing E. Dong

Rendered fromSpatialExperimentIO.Rmdusingknitr::rmarkdownon Feb 13 2025.

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