scDblFinder
This is the development version of scDblFinder; for the stable release version, see scDblFinder.
scDblFinder
Bioconductor version: Development (3.21)
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:
Maintainer: Pierre-Luc Germain <pierre-luc.germain at hest.ethz.ch>
citation("scDblFinder")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ATACSeq, Preprocessing, RNASeq, SingleCell, Software |
| Version | 1.21.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (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_1.21.0.tar.gz |
| Windows Binary (x86_64) | scDblFinder_1.21.0.zip (64-bit only) |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |