Utilities for Handling Single-Cell Droplet Data


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Documentation for package ‘DropletUtils’ version 1.18.1

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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