# Utilities for Handling Single-Cell Droplet Data

## Documentation for package ‘DropletUtils’ version 1.22.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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