scDblFinder

DOI: 10.18129/B9.bioc.scDblFinder    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see scDblFinder.

scDblFinder

Bioconductor version: 3.13

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

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 "4.1") and enter:

if (!requireNamespace("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		5_recoverDoublets
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Preprocessing, RNASeq, SingleCell, Software
Version	1.6.0
In Bioconductor since	BioC 3.10 (R-3.6) (2 years)
License	GPL-3
Depends	R (>= 4.1)
Imports	igraph, Matrix, BiocGenerics, BiocParallel, BiocNeighbors, BiocSingular, S4Vectors, SummarizedExperiment, SingleCellExperiment, scran, scater, scuttle, bluster, methods, DelayedArray, xgboost, stats, utils, mbkmeans
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat, scRNAseq, circlize, ComplexHeatmap, ggplot2, dplyr, MASS, viridisLite
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_1.6.0.tar.gz
Windows Binary	scDblFinder_1.6.0.zip
macOS 10.13 (High Sierra)	scDblFinder_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scDblFinder
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scDblFinder
Package Short Url	https://bioconductor.org/packages/scDblFinder/
Package Downloads Report	Download Stats