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>

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

Installation

To install this package, start R (version "4.1") 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")
1_introduction HTML R Script
2_scDblFinder HTML R Script
3_findDoubletClusters HTML R Script
4_computeDoubletDensity HTML R Script
5_recoverDoublets HTML
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Preprocessing, RNASeq, SingleCell, Software
Version 1.6.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 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
System Requirements
URL https://github.com/plger/scDblFinder
Bug Reports https://github.com/plger/scDblFinder/issues
See More
Suggests BiocStyle, knitr, rmarkdown, testthat, scRNAseq, circlize, ComplexHeatmap, ggplot2, dplyr, MASS, viridisLite
Linking To
Enhances
Depends On Me OSCA.advanced
Imports Me singleCellTK
Suggests Me
Links To Me
Build Report 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
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 3.13 Source Archive