Package: DoubletFinder 2.0.4

Chris McGinnis

DoubletFinder: DoubletFinder is a suite of tools for identifying doublets in single-cell RNA sequencing data.

DoubletFinder identifies doublets by generating artificial doublets from existing scRNA-seq data and defining which real cells preferentially co-localize with artificial doublets in gene expression space. Other DoubletFinder package functions are used for fitting DoubletFinder to different scRNA-seq datasets. For example, ideal DoubletFinder performance in real-world contexts requires (I) Optimal pK selection and (2) Homotypic doublet proportion estimation. pK selection is achieved using pN-pK parameter sweeps and maxima identification in mean-variance-normalized bimodality coefficient distributions. Homotypic doublet proportion estimation is achieved by finding the sum of squared cell annotation frequencies. For more information, see our Cell Sysmtes paper https://www.cell.com/cell-systems/fulltext/S2405-4712(19)30073-0 and our github https://github.com/chris-mcginnis-ucsf/DoubletFinder

Authors:Chris McGinnis [aut, cre]

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DoubletFinder.pdf |DoubletFinder.html✨
DoubletFinder/json (API)

Peer review:

Bug tracker:https://github.com/blaserlab/doubletfinder/issues

On CRAN:

9 exports 1.24 score 12 dependencies 1 dependents 876 scripts

Last updated 7 months agofrom:cff84e94d5. Checks:OK: 1 ERROR: 6. Indexed: yes.

Exports:bimodality_coefficientdoubletFinderfind.pKkurtosismodelHomotypicparallel_paramSweepparamSweepskewnesssummarizeSweep

Dependencies:bitopscaToolsdotCall64fieldsgplotsgtoolsKernSmoothmapsRcppROCRspamviridisLite