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.
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datarepresentationdataimportinfrastructuretranscriptomicssinglecellspatialgeneexpression
6.65 score 19 stars 1 dependents 78 scripts 408 downloadsOSTA.data - OSTA book data
'OSTA.data' is a companion package for the "Orchestrating Spatial Transcriptomics Analysis" (OSTA) with Bioconductor online book. Throughout OSTA, we rely on a set of publicly available datasets that cover different sequencing- and imaging-based platforms, such as Visium, Visium HD, Xenium (10x Genomics) and CosMx (NanoString). In addition, we rely on scRNA-seq (Chromium) data for tasks, e.g., spot deconvolution and label transfer (i.e., supervised clustering). These data been deposited in an Open Storage Framework (OSF) repository, and can be queried and downloaded using functions from the 'osfr' package. For convenience, we have implemented 'OSTA.data' to query and retrieve data from our OSF node, and cache retrieved Zip archives using 'BiocFileCache'.
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dataimportdatarepresentationexperimenthubsoftwareinfrastructureimmunooncologygeneexpressiontranscriptomicssinglecellspatial
6.56 score 2 stars 1 dependents 153 scripts 393 downloads