Package: scDblFinder 1.21.0
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_1.21.0.tar.gz
scDblFinder_1.21.0.zip(r-4.5)scDblFinder_1.21.0.zip(r-4.4)scDblFinder_1.21.0.zip(r-4.3)
scDblFinder_1.21.0.tgz(r-4.4-any)scDblFinder_1.21.0.tgz(r-4.3-any)
scDblFinder_1.21.0.tar.gz(r-4.5-noble)scDblFinder_1.21.0.tar.gz(r-4.4-noble)
scDblFinder_1.21.0.tgz(r-4.4-emscripten)scDblFinder_1.21.0.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
On BioConductor:scDblFinder-1.21.0(bioc 3.21)scDblFinder-1.20.0(bioc 3.20)
preprocessingsinglecellrnaseqatacseqdoubletssingle-cell
Last updated 22 days agofrom:4c44445515. Checks:OK: 1 NOTE: 4 ERROR: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win | NOTE | Oct 31 2024 |
| R-4.5-linux | NOTE | Oct 31 2024 |
| R-4.4-win | NOTE | Oct 31 2024 |
| R-4.4-mac | ERROR | Oct 31 2024 |
| R-4.3-win | NOTE | Oct 31 2024 |
| R-4.3-mac | ERROR | Oct 31 2024 |
Exports:addDoubletsaggregateFeaturesamuletamuletFromCountsclamuletclusterStickinesscomputeDoubletDensitycreateDoubletscxds2directDblClassificationdoubletPairwiseEnrichmentdoubletThresholdingfastclusterfindDoubletClustersgetArtificialDoubletsgetCellPairsgetExpectedDoubletsgetFragmentOverlapsmockDoubletSCEplotDoubletMapplotThresholdspropHomotypicrecoverDoubletsscDblFinderselFeaturesTFIDF
Dependencies:abindaskpassassortheadbeachmatbeeswarmBHBiobaseBiocGenericsBiocIOBiocNeighborsBiocParallelBiocSingularBiostringsbitopsblusterCairocliclustercodetoolscolorspacecpp11crayoncurldata.tableDelayedArraydqrngedgeRfansifarverFNNformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggbeeswarmggplot2ggrastrggrepelgluegridExtragtablehttrigraphIRangesirlbaisobandjsonlitelabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmetapodmgcvmimemunsellnlmeopensslpheatmappillarpkgconfigpngR6raggRColorBrewerRcppRcppAnnoyRcppEigenRcppMLRcppProgressRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSpectrarsvdrtracklayerRtsneS4ArraysS4VectorsScaledMatrixscalesscaterscranscuttleSingleCellExperimentsitmosnowSparseArraystatmodSummarizedExperimentsyssystemfontstextshapingtibbleUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrxgboostXMLXVectoryamlzlibbioc
Introduction to the scDblFinder package
Rendered fromintroduction.Rmdusingknitr::rmarkdownon Oct 31 2024.Last update: 2024-10-18
Started: 2020-09-07
scDblFinder
Rendered fromscDblFinder.Rmdusingknitr::rmarkdownon Oct 31 2024.Last update: 2024-10-18
Started: 2019-05-23
Detecting clusters of doublet cells with DE analyses
Rendered fromfindDoubletClusters.Rmdusingknitr::rmarkdownon Oct 31 2024.Last update: 2021-04-19
Started: 2020-07-20
Scoring potential doublets from simulated densities
Rendered fromcomputeDoubletDensity.Rmdusingknitr::rmarkdownon Oct 31 2024.Last update: 2021-04-19
Started: 2020-08-04
Recovering intra-sample doublets
Rendered fromrecoverDoublets.Rmdusingknitr::rmarkdownon Oct 31 2024.Last update: 2021-09-10
Started: 2020-09-08
Doublet identifiation in single-cell ATAC-seq
Rendered fromscATAC.Rmdusingknitr::rmarkdownon Oct 31 2024.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 |
