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scDblFinder

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

scDblFinder


Bioconductor version: Development (3.19)

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 "4.4") and enter:


if (!require("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")
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 HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews ATACSeq, Preprocessing, RNASeq, SingleCell, Software
Version 1.17.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 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
System Requirements
URL https://github.com/plger/scDblFinder https://plger.github.io/scDblFinder/
Bug Reports https://github.com/plger/scDblFinder/issues
See More
Suggests BiocStyle, knitr, rmarkdown, testthat, scRNAseq, circlize, ComplexHeatmap, ggplot2, dplyr, viridisLite, mbkmeans
Linking To
Enhances
Depends On Me
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_1.17.0.tar.gz
Windows Binary scDblFinder_1.17.0.zip
macOS Binary (x86_64) scDblFinder_1.17.0.tgz
macOS Binary (arm64) scDblFinder_1.17.0.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