Package: scDblFinder 1.27.12
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_1.27.12.tar.gz
scDblFinder_1.27.12.zip(r-4.7-any)scDblFinder_1.27.12.zip(r-4.6-any)scDblFinder_1.27.12.zip(r-4.5-any)
scDblFinder_1.27.12.tgz(r-4.6-any)scDblFinder_1.27.12.tgz(r-4.5-any)
scDblFinder_1.27.12.tar.gz(r-4.7-any)scDblFinder_1.27.12.tar.gz(r-4.6-any)
scDblFinder_1.27.12.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
scDblFinder/json (API)
| # 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/docs site:https://plger.github.io
On BioConductor:scDblFinder-1.27.12(bioc 3.24)scDblFinder-1.26.9(bioc 3.23)
preprocessingsinglecellrnaseqatacseqdoubletssingle-cell
Last updated from:e66180a1d8. Checks:8 WARNING, 1 ERROR, 1 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 233 | ||
| linux-devel | WARNING | 605 | ||
| source / vignettes | ERROR | 400 | ||
| linux-release | WARNING | 510 | ||
| macos-release | WARNING | 421 | ||
| macos-oldrel | WARNING | 452 | ||
| windows-devel | WARNING | 622 | ||
| windows-release | WARNING | 630 | ||
| windows-oldrel | WARNING | 1470 | ||
| wasm-release | OK | 163 |
Exports:addDoubletsaggregateFeaturesamuletamuletFromCountsclamuletclusterStickinesscomputeDoubletDensitycreateDoubletscxds2directDblClassificationdoubletPairwiseEnrichmentdoubletThresholdingfastclusterfindDoubletClustersgetArtificialDoubletsgetCellPairsgetExpectedDoubletsgetFragmentOverlapsidentifyDoubletOriginsmockDoubletSCEplotDoubletMapplotThresholdspredictDoubletOriginspropHomotypicrecoverDoubletsscDblFinderselFeaturessmoothDoubletScoresTFIDF
Dependencies:abindaskpassassortheadbeachmatbeeswarmBHBiobaseBiocBaseUtilsBiocGenericsBiocIObiocmakeBiocNeighborsBiocParallelBiocSingularBiostringsbitopsblustercigarillocliclustercodetoolscpp11crayoncurldata.tableDelayedArraydir.expirydqrngfarverfilelockFNNformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicRangesggbeeswarmggplot2ggrepelgluegridExtragtablehttrigraphIRangesirlbaisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmimeopensslpheatmappkgconfigR6RColorBrewerRcppRcppAnnoyRcppEigenRcppMLRcppProgressRCurlrestfulrRhtslibRigraphlibrjsonrlangRsamtoolsRSpectrarsvdrtracklayerRtsneS4ArraysS4VectorsS7ScaledMatrixscalesscaterscrapperscuttleSeqinfoSingleCellExperimentsitmosnowSparseArraySummarizedExperimentsysUCSC.utilsuwotvctrsviporviridisviridisLitewithrxgboostXMLXVectoryaml
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 |
| identifyDoubletOrigins | identifyDoubletOrigins |
| mockDoubletSCE | mockDoubletSCE |
| plotDoubletMap | plotDoubletMap |
| plotThresholds | plotThresholds |
| predictDoubletOrigins : run an origins classifier on new cells | predictDoubletOrigins |
| propHomotypic | propHomotypic |
| Recover intra-sample doublets | recoverDoublets recoverDoublets,ANY-method recoverDoublets,SingleCellExperiment-method recoverDoublets,SummarizedExperiment-method |
| scDblFinder | scDblFinder |
| selFeatures | selFeatures |
| Smooth Doublet Scores | smoothDoubletScores |
| TFIDF | TFIDF |