Package: scDblFinder 1.21.1
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_1.21.1.tar.gz
scDblFinder_1.21.1.zip(r-4.5)scDblFinder_1.21.1.zip(r-4.4)scDblFinder_1.21.1.zip(r-4.3)
scDblFinder_1.21.1.tgz(r-4.5-any)scDblFinder_1.21.1.tgz(r-4.4-any)scDblFinder_1.21.1.tgz(r-4.3-any)
scDblFinder_1.21.1.tar.gz(r-4.5-noble)scDblFinder_1.21.1.tar.gz(r-4.4-noble)
scDblFinder_1.21.1.tgz(r-4.4-emscripten)scDblFinder_1.21.1.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-1.20.0(bioc 3.20)
preprocessingsinglecellrnaseqatacseqdoubletssingle-cell
Last updated 2 months agofrom:a4900460ee. Checks:1 OK, 6 NOTE, 1 ERROR. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 08 2025 |
| R-4.5-win | NOTE | Feb 08 2025 |
| R-4.5-mac | NOTE | Feb 08 2025 |
| R-4.5-linux | NOTE | Feb 08 2025 |
| R-4.4-win | NOTE | Feb 08 2025 |
| R-4.4-mac | NOTE | Feb 08 2025 |
| R-4.3-win | NOTE | Feb 08 2025 |
| R-4.3-mac | ERROR | Jan 09 2025 |
Exports:addDoubletsaggregateFeaturesamuletamuletFromCountsclamuletclusterStickinesscomputeDoubletDensitycreateDoubletscxds2directDblClassificationdoubletPairwiseEnrichmentdoubletThresholdingfastclusterfindDoubletClustersgetArtificialDoubletsgetCellPairsgetExpectedDoubletsgetFragmentOverlapsmockDoubletSCEplotDoubletMapplotThresholdspropHomotypicrecoverDoubletsscDblFinderselFeaturesTFIDF
Dependencies:abindaskpassassortheadbeachmatbeeswarmBHBiobaseBiocGenericsBiocIOBiocNeighborsBiocParallelBiocSingularBiostringsbitopsblusterCairocliclustercodetoolscolorspacecpp11crayoncurldata.tableDelayedArraydqrngedgeRfansifarverFNNformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggbeeswarmggplot2ggrastrggrepelgluegridExtragtablehttrigraphIRangesirlbaisobandjsonlitelabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmetapodmgcvmimemunsellnlmeopensslpheatmappillarpkgconfigpngR6raggRColorBrewerRcppRcppAnnoyRcppEigenRcppMLRcppProgressRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSpectrarsvdrtracklayerRtsneS4ArraysS4VectorsScaledMatrixscalesscaterscranscuttleSingleCellExperimentsitmosnowSparseArraystatmodstringiSummarizedExperimentsyssystemfontstextshapingtibbleUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrxgboostXMLXVectoryaml
Introduction to the scDblFinder package
Rendered fromintroduction.Rmdusingknitr::rmarkdownon Feb 08 2025.Last update: 2024-10-18
Started: 2020-09-07
scDblFinder
Rendered fromscDblFinder.Rmdusingknitr::rmarkdownon Feb 08 2025.Last update: 2024-10-18
Started: 2019-05-23
Detecting clusters of doublet cells with DE analyses
Rendered fromfindDoubletClusters.Rmdusingknitr::rmarkdownon Feb 08 2025.Last update: 2021-04-19
Started: 2020-07-20
Scoring potential doublets from simulated densities
Rendered fromcomputeDoubletDensity.Rmdusingknitr::rmarkdownon Feb 08 2025.Last update: 2021-04-19
Started: 2020-08-04
Recovering intra-sample doublets
Rendered fromrecoverDoublets.Rmdusingknitr::rmarkdownon Feb 08 2025.Last update: 2021-09-10
Started: 2020-09-08
Doublet identifiation in single-cell ATAC-seq
Rendered fromscATAC.Rmdusingknitr::rmarkdownon Feb 08 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 |
