scDblFinder

DOI: 10.18129/B9.bioc.scDblFinder    

scDblFinder

Bioconductor version: Release (3.15)

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>

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

Installation

To install this package, start R (version "4.2") 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 1.10.0
In Bioconductor since BioC 3.10 (R-3.6) (3 years)
License GPL-3 + file LICENSE
Depends R (>= 4.0)
Imports igraph, Matrix, BiocGenerics, BiocParallel, BiocNeighbors, BiocSingular, S4Vectors, SummarizedExperiment, SingleCellExperiment, 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_1.10.0.tar.gz
Windows Binary scDblFinder_1.10.0.zip (64-bit only)
macOS Binary (x86_64) scDblFinder_1.10.0.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

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