scDblFinder

DOI: 10.18129/B9.bioc.scDblFinder  

scDblFinder

Bioconductor version: Release (3.17)

The scDblFinder package gathers various methods for the detection and handling of doublets/multiplets in single-cell sequencing data (i.e. multiple cells captured within the same droplet or reaction volume). It includes methods formerly found in the scran package, the new fast and comprehensive scDblFinder method, and a reimplementation of the Amulet detection method for single-cell ATAC-seq.

Author: Pierre-Luc Germain [cre, aut] , Aaron Lun [ctb]

Maintainer: Pierre-Luc Germain <pierre-luc.germain at hest.ethz.ch>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("scDblFinder")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("scDblFinder")

 

HTML	R Script	1_introduction
HTML	R Script	2_scDblFinder
HTML	R Script	3_findDoubletClusters
HTML	R Script	4_computeDoubletDensity
HTML	R Script	5_recoverDoublets
HTML	R Script	6_scATAC
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	ATACSeq, Preprocessing, RNASeq, SingleCell, Software
Version	1.14.0
In Bioconductor since	BioC 3.10 (R-3.6) (4 years)
License	GPL-3 + file LICENSE
Depends	R (>= 4.0), SingleCellExperiment
Imports	igraph, Matrix, BiocGenerics, BiocParallel, BiocNeighbors, BiocSingular, S4Vectors, SummarizedExperiment, scran, scater, scuttle, bluster, methods, DelayedArray, xgboost, stats, utils, MASS, IRanges, GenomicRanges, GenomeInfoDb, Rsamtools, rtracklayer
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat, scRNAseq, circlize, ComplexHeatmap, ggplot2, dplyr, viridisLite, mbkmeans
SystemRequirements
Enhances
URL	https://github.com/plger/scDblFinder
BugReports	https://github.com/plger/scDblFinder/issues
Depends On Me	OSCA.advanced
Imports Me	singleCellTK
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	scDblFinder_1.14.0.tar.gz
Windows Binary	scDblFinder_1.14.0.zip
macOS Binary (x86_64)	scDblFinder_1.14.0.tgz
macOS Binary (arm64)	scDblFinder_1.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scDblFinder
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scDblFinder
Bioc Package Browser	https://code.bioconductor.org/browse/scDblFinder/
Package Short Url	https://bioconductor.org/packages/scDblFinder/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive