BatchSVG - Identify Batch-Biased Spatially Variable Genes
BatchSVG is a method to identify batch-biased spatially variable genes (SVGs) in spatial transcriptomics data. The batch variable can be defined as sample, donor sex, or other batch effects of interest. The BatchSVG method is based on the binomial deviance model (Townes et al, 2019).
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spatialtranscriptomicsbatcheffectqualitycontrolbatch-effectbioconductor-packagespatial-transcriptomics
5.47 score 5 stars 13 scripts 269 downloadsspoon - Address the Mean-variance Relationship in Spatial Transcriptomics Data
This package addresses the mean-variance relationship in spatially resolved transcriptomics data. Precision weights are generated for individual observations using Empirical Bayes techniques. These weights are used to rescale the data and covariates, which are then used as input in spatially variable gene detection tools.
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spatialsinglecelltranscriptomicsgeneexpressionpreprocessing
4.38 score 24 scripts 294 downloadsspatialSimGP - Simulate Spatial Transcriptomics Data with the Mean-variance Relationship
This packages simulates spatial transcriptomics data with the mean- variance relationship using a Gaussian Process model per gene.
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spatialtranscriptomicsgeneexpression
4.00 score 2 scripts 254 downloads