scDblFinder
This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see scDblFinder.
scDblFinder
Bioconductor version: 3.14
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("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 | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Preprocessing, RNASeq, SingleCell, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (4.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.0) |
| Imports | igraph, Matrix, BiocGenerics, BiocParallel, BiocNeighbors, BiocSingular, S4Vectors, SummarizedExperiment, SingleCellExperiment, scran, scater, scuttle, bluster, methods, DelayedArray, xgboost, stats, utils, MASS |
| 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, mbkmeans |
| 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_1.8.0.tar.gz |
| Windows Binary | scDblFinder_1.8.0.zip |
| macOS 10.13 (High Sierra) | scDblFinder_1.8.0.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 3.14 | Source Archive |