spacexr

Transcriptomics analysis tool

Software package for cell type identification and differential expression in spatial transcriptomics

Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics

GitHub

322 stars
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last commit: over 2 years ago
cell-type-identificationdifferential-expressionspatial-transcriptomics

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