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]

DoubletFinder_2.0.4.tar.gz
DoubletFinder_2.0.4.zip(r-4.5)DoubletFinder_2.0.4.zip(r-4.4)DoubletFinder_2.0.4.zip(r-4.3)
DoubletFinder_2.0.4.tgz(r-4.4-any)DoubletFinder_2.0.4.tgz(r-4.3-any)
DoubletFinder_2.0.4.tar.gz(r-4.5-noble)DoubletFinder_2.0.4.tar.gz(r-4.4-noble)
DoubletFinder_2.0.4.tgz(r-4.4-emscripten)DoubletFinder_2.0.4.tgz(r-4.3-emscripten)
DoubletFinder.pdf |DoubletFinder.html
DoubletFinder/json (API)

# Install 'DoubletFinder' in R:
install.packages('DoubletFinder', repos = c('https://blaserlab.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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

On CRAN:

9 exports 1.24 score 12 dependencies 1 dependents

Last updated 5 months agofrom:cff84e94d5

Exports:bimodality_coefficientdoubletFinderfind.pKkurtosismodelHomotypicparallel_paramSweepparamSweepskewnesssummarizeSweep

Dependencies:bitopscaToolsdotCall64fieldsgplotsgtoolsKernSmoothmapsRcppROCRspamviridisLite

Readme and manuals

Help Manual

Help pageTopics
bimodality_coefficientbimodality_coefficient
doubletFinderdoubletFinder
find.pKfind.pK
kurtosiskurtosis
modelHomotypicmodelHomotypic
parallel_paramSweepparallel_paramSweep
paramSweepparamSweep
skewnessskewness
summarizeSweepsummarizeSweep