zijianni/SpotClean: SpotClean adjusts for spot swapping in spatial transcriptomics data

SpotClean is a computational method to adjust for spot swapping in spatial transcriptomics data. Recent spatial transcriptomics experiments utilize slides containing thousands of spots with spot-specific barcodes that bind mRNA. Ideally, unique molecular identifiers at a spot measure spot-specific expression, but this is often not the case due to bleed from nearby spots, an artifact we refer to as spot swapping. SpotClean is able to estimate the contamination rate in observed data and decontaminate the spot swapping effect, thus increase the sensitivity and precision of downstream analyses.

Getting started

Package details

Bioconductor views DataImport GeneExpression Preprocessing RNASeq Sequencing SingleCell Spatial Transcriptomics
URL https://github.com/zijianni/SpotClean
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
zijianni/SpotClean documentation built on June 12, 2024, 1:58 a.m.