A DoubletFinder workflow | 1. Choose pK | 2. Estimate the number of doublets | 3. Call doublets | Lower-level functions | Threads | Reference
Package: doubletrs 0.1.0
Mayank Gandhi
doubletrs: Memory-Efficient Doublet Detection for Single-Cell RNA Sequencing
Detects doublets in single-cell RNA sequencing data with the 'DoubletFinder' method of McGinnis, Murrow and Gartner (2019) <doi:10.1016/j.cels.2019.03.003>, implemented in 'Rust' to use less memory and time. Provides artificial doublet simulation, exact nearest-neighbour search and pANN (proportion of artificial nearest neighbours) scoring, and reproduces 'DoubletFinder' scores exactly.
Authors:
doubletrs_0.1.0.tar.gz
doubletrs_0.1.0.zip(r-4.7-x86_64)doubletrs_0.1.0.zip(r-4.7-arm64)doubletrs_0.1.0.zip(r-4.6-x86_64)doubletrs_0.1.0.zip(r-4.6-arm64)
doubletrs_0.1.0.tar.gz(r-4.7-arm64)doubletrs_0.1.0.tar.gz(r-4.7-x86_64)doubletrs_0.1.0.tar.gz(r-4.6-arm64)doubletrs_0.1.0.tar.gz(r-4.6-x86_64)
doubletrs_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
doubletrs/json (API)
| # Install 'doubletrs' in R: |
| install.packages('doubletrs', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mayankgandhi13/doublet-rs/issues
Last updated from:8223523bee. Checks:10 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 206 | ||
| linux-devel-x86_64 | OK | 180 | ||
| source / vignettes | OK | 282 | ||
| linux-release-arm64 | OK | 174 | ||
| linux-release-x86_64 | OK | 214 | ||
| windows-devel-arm64 | OK | 362 | ||
| windows-devel-x86_64 | OK | 247 | ||
| windows-release-arm64 | OK | 359 | ||
| windows-release-x86_64 | OK | 204 | ||
| wasm-release | OK | 191 |
Exports:compute_panndoubletFinderdoubletrs_threadsfind_neighborsfind.pKmodelHomotypicparamSweepsimulate_doubletssummarizeSweep
Dependencies:KernSmoothlatticeMatrix
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Compute pANN scores | compute_pann |
| Detect doublets in a Seurat object | doubletFinder |
| Number of threads used by doubletrs | doubletrs_threads |
| Find nearest neighbours of real cells | find_neighbors |
| Choose pK from a parameter sweep | find.pK |
| Estimate the proportion of homotypic doublets | modelHomotypic |
| pN-pK parameter sweep | paramSweep |
| Simulate artificial doublets | simulate_doublets |
| Summarise a parameter sweep | summarizeSweep |