sketchR

This is the development version of sketchR; for the stable release version, see sketchR.

An R interface for python subsampling/sketching algorithms

Bioconductor version: Development (3.21)

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] (ORCID: ), Michael Stadler [aut] (ORCID: ), 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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	SingleCell, Software
Version	1.1.3
In Bioconductor since	BioC 3.19 (R-4.4) (0.5 years)
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

Suggests	rmarkdown, knitr, testthat (>= 3.0.0), TENxPBMCData, scuttle, scran, scater, SingleR, celldex, cowplot, SummarizedExperiment, beachmat.hdf5, BiocStyle, BiocManager, SingleCellExperiment
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	sketchR_1.1.3.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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