ambientContribMaximum | Ambient contribution by maximum scaling |
ambientContribMaximum-method | Ambient contribution by maximum scaling |
ambientContribNegative | Ambient contribution from negative controls |
ambientContribNegative-method | Ambient contribution from negative controls |
ambientContribSparse | Ambient contribution by assuming sparsity |
ambientContribSparse-method | Ambient contribution by assuming sparsity |
ambientProfileBimodal | Ambient profile from bimodality |
ambientProfileBimodal-method | Ambient profile from bimodality |
ambientProfileEmpty | Estimate the ambient profile from empty droplets |
ambientProfileEmpty-method | Estimate the ambient profile from empty droplets |
barcodeRanks | Calculate barcode ranks |
barcodeRanks-method | Calculate barcode ranks |
chimericDrops | Remove chimeric molecules |
cleanTagCounts | Clean a tag-based dataset |
cleanTagCounts-method | Clean a tag-based dataset |
controlAmbience | Ambient contribution from negative controls |
defaultDrops | Call cells from their total number of UMIs |
defaultDrops-method | Call cells from their total number of UMIs |
downsampleReads | Downsample reads in a 10X Genomics dataset |
emptyDrops | Identify empty droplets |
emptyDrops-method | Identify empty droplets |
emptyDropsCellRanger | CellRanger's emptyDrops variant |
emptyDropsCellRanger-method | CellRanger's emptyDrops variant |
encodeSequences | Encode nucleotide sequences |
estimateAmbience | Estimate the ambient profile from empty droplets |
get10xMolInfoStats | Get 10x cell statistics |
hashedDrops | Demultiplex cell hashing data |
hashedDrops-method | Demultiplex cell hashing data |
inferAmbience | Ambient profile from bimodality |
makeCountMatrix | Make a count matrix |
maximumAmbience | Ambient contribution by maximum scaling |
read10xCounts | Load data from a 10X Genomics experiment |
read10xMolInfo | Read the 10X molecule information file |
removeAmbience | Remove the ambient profile |
removeAmbience-method | Remove the ambient profile |
removeChimericDrops | Remove chimeric molecules |
removeSwappedDrops | Clean barcode-swapped droplet data |
swappedDrops | Clean barcode-swapped droplet data |
testEmptyDrops | Identify empty droplets |
write10xCounts | Write count data in the 10x format |