Package: scDblFinder 1.21.2
Pierre-Luc Germain
scDblFinder: scDblFinder
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.
Authors:
scDblFinder_1.21.2.tar.gz
scDblFinder_1.21.2.zip(r-4.5)scDblFinder_1.21.2.zip(r-4.4)scDblFinder_1.21.2.zip(r-4.3)
scDblFinder_1.21.2.tgz(r-4.5-any)scDblFinder_1.21.2.tgz(r-4.4-any)scDblFinder_1.21.2.tgz(r-4.3-any)
scDblFinder_1.21.2.tar.gz(r-4.5-noble)scDblFinder_1.21.2.tar.gz(r-4.4-noble)
scDblFinder_1.21.2.tgz(r-4.4-emscripten)scDblFinder_1.21.2.tgz(r-4.3-emscripten)
scDblFinder.pdf |scDblFinder.html✨
scDblFinder/json (API)
NEWS
| # Install 'scDblFinder' in R: |
| install.packages('scDblFinder', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/plger/scdblfinder/issues
Pkgdown site:https://plger.github.io
On BioConductor:scDblFinder-1.21.1(bioc 3.21)scDblFinder-1.20.2(bioc 3.20)
preprocessingsinglecellrnaseqatacseqdoubletssingle-cell
Last updated 21 hours agofrom:b223a7db75. Checks:1 OK, 7 NOTE, 1 ERROR. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 21 2025 |
| R-4.5-win | NOTE | Mar 21 2025 |
| R-4.5-mac | NOTE | Mar 21 2025 |
| R-4.5-linux | NOTE | Mar 21 2025 |
| R-4.4-win | NOTE | Mar 21 2025 |
| R-4.4-mac | NOTE | Mar 21 2025 |
| R-4.4-linux | NOTE | Mar 21 2025 |
| R-4.3-win | NOTE | Mar 21 2025 |
| R-4.3-mac | ERROR | Mar 21 2025 |
Exports:addDoubletsaggregateFeaturesamuletamuletFromCountsclamuletclusterStickinesscomputeDoubletDensitycreateDoubletscxds2directDblClassificationdoubletPairwiseEnrichmentdoubletThresholdingfastclusterfindDoubletClustersgetArtificialDoubletsgetCellPairsgetExpectedDoubletsgetFragmentOverlapsmockDoubletSCEplotDoubletMapplotThresholdspropHomotypicrecoverDoubletsscDblFinderselFeaturesTFIDF
Dependencies:abindaskpassassortheadbeachmatbeeswarmBHBiobaseBiocGenericsBiocIOBiocNeighborsBiocParallelBiocSingularBiostringsbitopsblusterCairocliclustercodetoolscolorspacecpp11crayoncurldata.tableDelayedArraydqrngedgeRfansifarverFNNformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggbeeswarmggplot2ggrastrggrepelgluegridExtragtablehttrigraphIRangesirlbaisobandjsonlitelabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmetapodmgcvmimemunsellnlmeopensslpheatmappillarpkgconfigpngR6raggRColorBrewerRcppRcppAnnoyRcppEigenRcppMLRcppProgressRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSpectrarsvdrtracklayerRtsneS4ArraysS4VectorsScaledMatrixscalesscaterscranscuttleSingleCellExperimentsitmosnowSparseArraystatmodstringiSummarizedExperimentsyssystemfontstextshapingtibbleUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrxgboostXMLXVectoryaml
Introduction to the scDblFinder package
Rendered fromintroduction.Rmdusingknitr::rmarkdownon Mar 21 2025.Last update: 2024-10-18
Started: 2020-09-07
scDblFinder
Rendered fromscDblFinder.Rmdusingknitr::rmarkdownon Mar 21 2025.Last update: 2025-03-20
Started: 2019-05-23
Detecting clusters of doublet cells with DE analyses
Rendered fromfindDoubletClusters.Rmdusingknitr::rmarkdownon Mar 21 2025.Last update: 2021-04-19
Started: 2020-07-20
Scoring potential doublets from simulated densities
Rendered fromcomputeDoubletDensity.Rmdusingknitr::rmarkdownon Mar 21 2025.Last update: 2021-04-19
Started: 2020-08-04
Recovering intra-sample doublets
Rendered fromrecoverDoublets.Rmdusingknitr::rmarkdownon Mar 21 2025.Last update: 2021-09-10
Started: 2020-09-08
Doublet identifiation in single-cell ATAC-seq
Rendered fromscATAC.Rmdusingknitr::rmarkdownon Mar 21 2025.Last update: 2023-07-08
Started: 2022-04-10
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| addDoublets | addDoublets |
| aggregateFeatures | aggregateFeatures |
| amulet | amulet |
| amuletFromCounts | amuletFromCounts |
| clamulet | clamulet |
| clusterStickiness | clusterStickiness |
| Compute the density of simulated doublets | computeDoubletDensity computeDoubletDensity,ANY-method computeDoubletDensity,SingleCellExperiment-method computeDoubletDensity,SummarizedExperiment-method |
| createDoublets | createDoublets |
| cxds2 | cxds2 |
| directClassification | directDblClassification |
| doubletPairwiseEnrichment | doubletPairwiseEnrichment |
| doubletThresholding | doubletThresholding |
| fastcluster | fastcluster |
| Detect doublet clusters | findDoubletClusters findDoubletClusters,ANY-method findDoubletClusters,SingleCellExperiment-method findDoubletClusters,SummarizedExperiment-method |
| getArtificialDoublets | getArtificialDoublets |
| getCellPairs | getCellPairs |
| getExpectedDoublets | getExpectedDoublets |
| getFragmentOverlaps | getFragmentOverlaps |
| mockDoubletSCE | mockDoubletSCE |
| plotDoubletMap | plotDoubletMap |
| plotThresholds | plotThresholds |
| propHomotypic | propHomotypic |
| Recover intra-sample doublets | recoverDoublets recoverDoublets,ANY-method recoverDoublets,SingleCellExperiment-method recoverDoublets,SummarizedExperiment-method |
| scDblFinder | scDblFinder |
| selFeatures | selFeatures |
| TFIDF | TFIDF |
