Package: DropletUtils 1.25.0
Jonathan Griffiths
DropletUtils: Utilities for Handling Single-Cell Droplet Data
Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading from count matrices or molecule information files, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.
Authors:
DropletUtils_1.25.0.tar.gz
DropletUtils_1.25.0.zip(r-4.5)DropletUtils_1.25.0.zip(r-4.4)DropletUtils_1.25.0.zip(r-4.3)
DropletUtils_1.25.0.tgz(r-4.4-arm64)DropletUtils_1.25.0.tgz(r-4.4-x86_64)DropletUtils_1.25.0.tgz(r-4.3-arm64)DropletUtils_1.25.0.tgz(r-4.3-x86_64)
DropletUtils_1.25.0.tar.gz(r-4.5-noble)DropletUtils_1.25.0.tar.gz(r-4.4-noble)
DropletUtils.pdf |DropletUtils.html✨
DropletUtils/json (API)
NEWS
| # Install 'DropletUtils' in R: |
| install.packages('DropletUtils', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:DropletUtils-1.25.0(bioc 3.20)DropletUtils-1.24.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:09b8cf7761
Exports:ambientContribMaximumambientContribNegativeambientContribSparseambientProfileBimodalambientProfileEmptybarcodeRankschimericDropscleanTagCountscontrolAmbiencedefaultDropsdownsampleBatchesdownsampleMatrixdownsampleReadsemptyDropsemptyDropsCellRangerencodeSequencesestimateAmbienceget10xMolInfoStatshashedDropsinferAmbiencemakeCountMatrixmaximumAmbienceread10xCountsread10xMolInforemoveAmbienceremoveChimericDropsremoveSwappedDropsswappedDropstestEmptyDropswrite10xCounts
Dependencies:abindaskpassbeachmatBHBiobaseBiocGenericsBiocParallelcodetoolscpp11crayoncurlDelayedArrayDelayedMatrixStatsdqrngedgeRformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangesHDF5ArrayhttrIRangesjsonlitelambda.rlatticelimmalocfitMatrixMatrixGenericsmatrixStatsmimeopensslR.methodsS3R.ooR.utilsR6Rcpprhdf5rhdf5filtersRhdf5libS4ArraysS4VectorsscuttleSingleCellExperimentsitmosnowSparseArraysparseMatrixStatsstatmodSummarizedExperimentsysUCSC.utilsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Ambient contribution by maximum scaling | ambientContribMaximum ambientContribMaximum,ANY-method ambientContribMaximum,SummarizedExperiment-method maximumAmbience |
| Ambient contribution from negative controls | ambientContribNegative ambientContribNegative,ANY-method ambientContribNegative,SummarizedExperiment-method controlAmbience |
| Ambient contribution by assuming sparsity | ambientContribSparse ambientContribSparse,ANY-method ambientContribSparse,SummarizedExperiment-method |
| Ambient profile from bimodality | ambientProfileBimodal ambientProfileBimodal,ANY-method ambientProfileBimodal,SummarizedExperiment-method inferAmbience |
| Estimate the ambient profile from empty droplets | ambientProfileEmpty ambientProfileEmpty,ANY-method ambientProfileEmpty,SummarizedExperiment-method estimateAmbience |
| Calculate barcode ranks | barcodeRanks barcodeRanks,ANY-method barcodeRanks,SummarizedExperiment-method |
| Remove chimeric molecules | chimericDrops removeChimericDrops |
| Clean a tag-based dataset | cleanTagCounts cleanTagCounts,ANY-method cleanTagCounts,SummarizedExperiment-method |
| Call cells from their total number of UMIs | defaultDrops defaultDrops,ANY-method defaultDrops,SummarizedExperiment-method |
| Downsample reads in a 10X Genomics dataset | downsampleReads |
| Identify empty droplets | emptyDrops emptyDrops,ANY-method emptyDrops,SummarizedExperiment-method testEmptyDrops |
| CellRanger's emptyDrops variant | emptyDropsCellRanger emptyDropsCellRanger,ANY-method emptyDropsCellRanger,SummarizedExperiment-method |
| Encode nucleotide sequences | encodeSequences |
| Get 10x cell statistics | get10xMolInfoStats |
| Demultiplex cell hashing data | hashedDrops hashedDrops,ANY-method hashedDrops,SummarizedExperiment-method |
| Make a count matrix | makeCountMatrix |
| Load data from a 10X Genomics experiment | read10xCounts |
| Read the 10X molecule information file | read10xMolInfo |
| Remove the ambient profile | removeAmbience removeAmbience,ANY-method removeAmbience,SummarizedExperiment-method |
| Clean barcode-swapped droplet data | removeSwappedDrops swappedDrops |
| Write count data in the 10x format | write10xCounts |
