SpaNorm - Spatially-aware normalisation for spatial transcriptomics data
This package implements the spatially aware library size normalisation algorithm, SpaNorm. SpaNorm normalises out library size effects while retaining biology through the modelling of smooth functions for each effect. Normalisation is performed in a gene- and cell-/spot- specific manner, yielding library size adjusted data.
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softwaregeneexpressiontranscriptomicsspatialcellbiology
6.57 score 20 stars 31 scripts 356 downloadsSubcellularSpatialData - Annotated spatial transcriptomics datasets from 10x Xenium, NanoString CosMx and BGI STOmics.
This is a data package that hosts annotated sub-cellular localised datasets from the STOmics, Xenium and CosMx platforms. Specifically, it hosts datasets analysed in the publication Bhuva et. al, 2024 titled "Library size confounds biology in spatial transcriptomics data". Raw transcript detections are hosted and functions to convert them to SpatialExperiment objects have been implemented.
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experimenthubspatialdatahomo_sapiens_datamus_musculus_datalungcancerdatadatapkg
4.56 score 2 stars 18 scripts