scDblFinder

This is the released version of scDblFinder; for the devel version, see scDblFinder.

scDblFinder

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DOI: 10.18129/B9.bioc.scDblFinder

Bioconductor version: Release (3.22)

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] ORCID iD ORCID: 0000-0003-3418-4218 , 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 "4.5") 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 R Script

6_scATAC HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ATACSeq, Preprocessing, RNASeq, SingleCell, Software

Version 1.24.0

In Bioconductor since BioC 3.10 (R-3.6) (6 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

Suggests BiocStyle, knitr, rmarkdown, testthat, scRNAseq, circlize, ComplexHeatmap, ggplot2, dplyr, viridisLite, mbkmeans

Linking To

Enhances

Depends On Me OSCA.advanced

Imports Me DOtools, 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_1.24.0.tar.gz

Windows Binary (x86_64) scDblFinder_1.24.0.zip (64-bit only)

macOS Binary (x86_64) scDblFinder_1.24.0.tgz

macOS Binary (arm64) scDblFinder_1.24.0.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/

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