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.

Last updated 2 months ago

dataimportrnaseqsequencinggeneexpressionspatialsinglecelltranscriptomicspreprocessingrna-seqspatial-transcriptomics

6.43 score 25 stars 36 scripts 190 downloads

scCB2 - CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data

scCB2 is an R package implementing CB2 for distinguishing real cells from empty droplets in droplet-based single cell RNA-seq experiments (especially for 10x Chromium). It is based on clustering similar barcodes and calculating Monte-Carlo p-value for each cluster to test against background distribution. This cluster-level test outperforms single-barcode-level tests in dealing with low count barcodes and homogeneous sequencing library, while keeping FDR well controlled.

Last updated 2 months ago

dataimportrnaseqsinglecellsequencinggeneexpressiontranscriptomicspreprocessingclustering

5.30 score 10 stars 5 scripts 151 downloads