visium

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Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

workflow bioinformatics rna-seq pipeline nextflow image-processing spatial transcriptomics single-cell microscopy st 10x-genomics 10xgenomics nf-core spatial-transcriptomics visium

Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images

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