sketchR

An R interface for python subsampling/sketching algorithms


Bioconductor version: Release (3.19)

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.

Author: Charlotte Soneson [aut, cre] , Michael Stadler [aut] , Friedrich Miescher Institute for Biomedical Research [cph]

Maintainer: Charlotte Soneson <charlottesoneson at gmail.com>

Citation (from within R, enter citation("sketchR")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("sketchR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("sketchR")
sketchR HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews SingleCell, Software
Version 1.0.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License MIT + file LICENSE
Depends
Imports basilisk, Biobase, DelayedArray, dplyr, ggplot2, methods, reticulate, rlang, scales, stats
System Requirements
URL https://github.com/fmicompbio/sketchR
Bug Reports https://github.com/fmicompbio/sketchR/issues
See More
Suggests rmarkdown, knitr, testthat (>= 3.0.0), TENxPBMCData, scuttle, scran, scater, SingleR, celldex, cowplot, SummarizedExperiment, beachmat.hdf5, BiocStyle, BiocManager, SingleCellExperiment
Linking To
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package sketchR_1.0.0.tar.gz
Windows Binary (x86_64) sketchR_1.0.0.zip
macOS Binary (x86_64) sketchR_1.0.0.tgz
macOS Binary (arm64) sketchR_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/sketchR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/sketchR
Bioc Package Browser https://code.bioconductor.org/browse/sketchR/
Package Short Url https://bioconductor.org/packages/sketchR/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.19 Source Archive