Introduction | Reading in 10X Genomics data | From the UMI count matrix | From the molecule information file | Downsampling on the reads | Computing barcode ranks | Detecting empty droplets | Demultiplexing hashed libraries | Removing swapping effects | Barcode swapping between samples | Chimeric reads within cells | Session information
Package: DropletUtils 1.33.0
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_1.33.0.tar.gz
DropletUtils_1.33.0.zip(r-4.7)DropletUtils_1.33.0.zip(r-4.6)DropletUtils_1.33.0.zip(r-4.5)
DropletUtils_1.33.0.tgz(r-4.6-x86_64)DropletUtils_1.33.0.tgz(r-4.6-arm64)DropletUtils_1.33.0.tgz(r-4.5-x86_64)DropletUtils_1.33.0.tgz(r-4.5-arm64)
DropletUtils_1.33.0.tar.gz(r-4.7-arm64)DropletUtils_1.33.0.tar.gz(r-4.7-x86_64)DropletUtils_1.33.0.tar.gz(r-4.6-arm64)DropletUtils_1.33.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DropletUtils/json (API)
| # Install 'DropletUtils' in R: |
| install.packages('DropletUtils', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Uses libs:
On BioConductor:DropletUtils-1.33.0(bioc 3.24)DropletUtils-1.32.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologysinglecellsequencingrnaseqgeneexpressiontranscriptomicsdataimportcoveragecurlopensslcpp
Last updated from:ebff365ae1. Checks:1 NOTE, 3 ERROR, 1 OK, 8 WARNING, 1 FAIL. Indexed: yes.
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| bioc-checks | NOTE | 315 | ||
| linux-devel-arm64 | ERROR | 564 | ||
| linux-devel-x86_64 | ERROR | 609 | ||
| source / vignettes | OK | 523 | ||
| linux-release-arm64 | WARNING | 550 | ||
| linux-release-x86_64 | WARNING | 592 | ||
| macos-release-arm64 | WARNING | 397 | ||
| macos-release-x86_64 | WARNING | 573 | ||
| macos-oldrel-arm64 | WARNING | 388 | ||
| macos-oldrel-x86_64 | WARNING | 896 | ||
| windows-devel | ERROR | 1476 | ||
| windows-release | WARNING | 1394 | ||
| windows-oldrel | WARNING | 1219 | ||
| wasm-release | FAIL | 614 |
Exports:ambientContribMaximumambientContribNegativeambientContribSparseambientProfileBimodalambientProfileEmptybarcodeRankschimericDropscleanTagCountscontrolAmbiencedefaultDropsdownsampleBatchesdownsampleMatrixdownsampleReadsemptyDropsemptyDropsCellRangerencodeSequencesestimateAmbienceget10xMolInfoStatshashedDropsinferAmbiencemakeCountMatrixmaximumAmbienceread10xCountsread10xMolInforemoveAmbienceremoveChimericDropsremoveSwappedDropsswappedDropstestEmptyDropswrite10xCounts
Dependencies:abindassortheadbeachmatBHBiobaseBiocGenericsbiocmakeBiocParallelcodetoolscpp11DelayedArrayDelayedMatrixStatsdir.expirydqrngedgeRfilelockformatRfutile.loggerfutile.optionsgenericsGenomicRangesh5mreadHDF5ArrayIRangeslambda.rlatticelimmalocfitMatrixMatrixGenericsmatrixStatsR.methodsS3R.ooR.utilsRcpprhdf5rhdf5filtersRhdf5libS4ArraysS4VectorsscuttleSeqinfoSingleCellExperimentsitmosnowSparseArraysparseMatrixStatsstatmodSummarizedExperimentXVector
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 |
