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Bioconductor - sketchR

sketchR

This is the released version of sketchR; for the devel version, see sketchR.

An R interface for python subsampling/sketching algorithms

Bioconductor version: Release (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: 0000-0003-3833-2169 , Michael Stadler [aut] ORCID: 0000-0002-2269-4934 , 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")

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")
Details biocViews SingleCell, Software Version 1.4.0 In Bioconductor since BioC 3.19 (R-4.4) (1 year) 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 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.

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