scDblFinder

DOI: 10.18129/B9.bioc.scDblFinder    

This is the development version of scDblFinder; for the stable release version, see scDblFinder.

scDblFinder

Bioconductor version: Development (3.12)

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>

Citation (from within R, enter citation("scDblFinder")):

Installation

To install this package, start R (version "4.0") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 computeDoubletDensity
HTML R Script findDoubletClusters
HTML R Script introduction
HTML recoverDoublets
HTML R Script scDblFinder
PDF   Reference Manual
Text   LICENSE

Details

biocViews Preprocessing, RNASeq, SingleCell, Software
Version 1.3.9
In Bioconductor since BioC 3.10 (R-3.6) (1 year)
License GPL-3
Depends R (>= 4.0)
Imports igraph, Matrix, BiocGenerics, BiocParallel, BiocNeighbors, BiocSingular, S4Vectors, SummarizedExperiment, SingleCellExperiment, scran, scater, scuttle, methods, stats, DelayedArray, xgboost, stats, scds, intrinsicDimension, utils
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, testthat, scRNAseq, bluster
SystemRequirements
Enhances
URL https://github.com/plger/scDblFinder
BugReports https://github.com/plger/scDblFinder/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package scDblFinder_1.3.9.tar.gz
Windows Binary scDblFinder_1.3.9.zip
macOS 10.13 (High Sierra) scDblFinder_1.3.9.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

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