sketchR
An R interface for python subsampling/sketching algorithms
Bioconductor version: 3.24 · Package version: 1.9.1
Provides an R interface for various subsampling algorithms implemented in python packages. Currently, interfaces to the geosketch and scSampler python packages are implemented. In addition it also provides diagnostic plots to evaluate the subsampling.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("sketchR")Details
| Maintainer | Charlotte Soneson <charlottesoneson@gmail.com> |
| Author | Charlotte Soneson [aut, cre] (ORCID: <https://orcid.org/0000-0003-3833-2169>), Michael Stadler [aut] (ORCID: <https://orcid.org/0000-0002-2269-4934>), Friedrich Miescher Institute for Biomedical Research [cph] |
| License | MIT + file LICENSE |
| URL | https://github.com/fmicompbio/sketchR |
| Bug Reports | https://github.com/fmicompbio/sketchR/issues |
| Downloads rank | 358 |
| Source branch | devel |
| biocViews | SingleCell, Software |
Documentation
- Incorporating sketching into a typical single-cell analysis workflow
- Subsampling single-cell data sets with sketchR
Download
Follow the installation instructions to use this package in your R session.
| Source package | sketchR_1.9.1.tar.gz |
| Windows binary (x86_64) | sketchR_1.9.1.zip |
| macOS binary (arm64) | sketchR_1.9.1.tgz |
| macOS binary (x86_64) | sketchR_1.9.1.tgz |
Dependencies
Imports: basilisk, Biobase, DelayedArray, dplyr, ggplot2, methods, reticulate, rlang, scales, stats
Suggests: rmarkdown, knitr, testthat (>= 3.0.0), TENxPBMCData, scuttle, scater, SingleR, celldex, cowplot, SummarizedExperiment, beachmat.hdf5, BiocStyle, BiocManager, SingleCellExperiment, snifter, uwot, bluster, class, scrapper