BIOCONDUCTOR . ORG {
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Title:
Bioconductor - spacexr
Description:
Spatial-eXpression-R (spacexr) is a package for analyzing cell types in spatial transcriptomics data. This implementation is a fork of the spacexr GitHub repo (https://github.com/dmcable/spacexr), adapted to work with Bioconductor objects. The original package implements two statistical methods: RCTD for learning cell types and CSIDE for inferring cell type-specific differential expression. Currently, this fork only implements RCTD, which learns cell type profiles from annotated RNA sequencing (RNA-seq) reference data and uses these profiles to identify cell types in spatial transcriptomic pixels while accounting for platform-specific effects. Future releases will include an implementation of CSIDE.
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Keywords {🔍}
bioconductor, package, packages, spacexr, version, cell, spatial, release, source, transcriptomics, types, install, reports, binary, learn, developers, started, software, spatialexpressionr, type, data, implementation, fork, implements, methods, rctd, cside, profiles, rnaseq, reference, gabriel, grajeda, installation, start, enter, documentation, system, details, bioc, url, macos, spacexrtgz, repository, git, clone, code, registration, open, eurobioc, european,
Topics {✒️}
org/packages/spacexr source repository /ggrajeda/spacexr bug reports bioconductor release tgz source repository source package original package implements cell type identification european bioconductor conference platform-specific effects release //code analyzing cell types learning cell types identify cell types /ggrajeda/spacexr/issues bioconductor support site dylan cable [aut] gz windows binary zip macos binary tgz macos binary annotated rna sequencing script reference manual spatial transcriptomic pixels package installed git clone https details biocviews spatialexperiment system requirements spacexr github repo spatial transcriptomics data bioconductor objects packages spatial-expression started install package /dmcable/spacexr reference data bioconductor //bioconductor rna-seq transcriptomics version org implements rctd registration open future releases quietly = true older versions pdf news developer access download stats released version
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