Package: DoubletFinder 2.0.4
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:
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')) |
Bug tracker:https://github.com/blaserlab/doubletfinder/issues
Last updated 7 months agofrom:cff84e94d5. Checks:OK: 1 ERROR: 6. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Aug 14 2024 |
R-4.5-win | ERROR | Aug 14 2024 |
R-4.5-linux | ERROR | Aug 14 2024 |
R-4.4-win | ERROR | Aug 14 2024 |
R-4.4-mac | ERROR | Aug 14 2024 |
R-4.3-win | ERROR | Aug 14 2024 |
R-4.3-mac | ERROR | Aug 14 2024 |
Exports:bimodality_coefficientdoubletFinderfind.pKkurtosismodelHomotypicparallel_paramSweepparamSweepskewnesssummarizeSweep
Dependencies:bitopscaToolsdotCall64fieldsgplotsgtoolsKernSmoothmapsRcppROCRspamviridisLite
Readme and manuals
Help Manual
Help page | Topics |
---|---|
bimodality_coefficient | bimodality_coefficient |
doubletFinder | doubletFinder |
find.pK | find.pK |
kurtosis | kurtosis |
modelHomotypic | modelHomotypic |
parallel_paramSweep | parallel_paramSweep |
paramSweep | paramSweep |
skewness | skewness |
summarizeSweep | summarizeSweep |