scDblFinder
scDblFinder
Bioconductor version: 3.23 · Package version: 1.26.7
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("scDblFinder")Details
| Maintainer | Pierre-Luc Germain <pierre-luc.germain@hest.ethz.ch> |
| Author | Pierre-Luc Germain [cre, aut] (ORCID: <https://orcid.org/0000-0003-3418-4218>), Aaron Lun [ctb] |
| License | GPL-3 + file LICENSE |
| URL | https://github.com/plger/scDblFinder, https://plger.github.io/scDblFinder/ |
| Bug Reports | https://github.com/plger/scDblFinder/issues |
| Downloads rank | 4071 |
| Source branch | RELEASE_3_23 |
| biocViews | ATACSeq, Preprocessing, RNASeq, SingleCell, Software |
Documentation
- Introduction to the scDblFinder package
- scDblFinder
- Detecting clusters of doublet cells with DE analyses
- Scoring potential doublets from simulated densities
- Recovering intra-sample doublets
- Doublet identifiation in single-cell ATAC-seq
Download
Dependencies
Depends: R (>= 4.0), SingleCellExperiment
Imports: igraph, Matrix, BiocGenerics, BiocParallel, BiocNeighbors, BiocSingular, S4Vectors, SummarizedExperiment, scater, scuttle, scrapper, scran, bluster, methods, DelayedArray, xgboost (>= 3.1), stats, utils, MASS, IRanges, GenomicRanges, GenomeInfoDb, Rsamtools, rtracklayer
Suggests: BiocStyle, knitr, rmarkdown, testthat, scRNAseq, circlize, ComplexHeatmap, ggplot2, dplyr, viridisLite, mbkmeans
Reverse dependencies
Imports Me (2): DOtools, singleCellTK