Package: sketchR 1.3.0

Charlotte Soneson

sketchR: An R interface for python subsampling/sketching algorithms

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.

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

sketchR_1.3.0.tar.gz
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sketchR.pdf |sketchR.html✨
sketchR/json (API)
NEWS

# Install 'sketchR' in R:

install.packages('sketchR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/fmicompbio/sketchr/issues

On BioConductor:sketchR-1.1.3(bioc 3.21)sketchR-1.2.0(bioc 3.20)

singlecell

5.34 score 2 stars 3 scripts 194 downloads 6 exports 56 dependencies

Last updated 23 days agofrom:87da4c7253. Checks:OK: 1 NOTE: 3 WARNING: 3. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win	WARNING	Oct 31 2024
R-4.5-linux	NOTE	Oct 31 2024
R-4.4-win	WARNING	Oct 31 2024
R-4.4-mac	NOTE	Oct 31 2024
R-4.3-win	WARNING	Oct 31 2024
R-4.3-mac	NOTE	Oct 31 2024

Exports:compareCompositionPlot geosketch getGeosketchNames getScSamplerNames hausdorffDistPlot scsampler

Dependencies:abind basilisk basilisk.utils Biobase BiocGenerics cli colorspace crayon DelayedArray dir.expiry dplyr fansi farver filelock generics ggplot2 glue gtable here IRanges isoband jsonlite labeling lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mgcv munsell nlme pillar pkgconfig png R6 rappdirs RColorBrewer Rcpp RcppTOML reticulate rlang rprojroot S4Arrays S4Vectors scales SparseArray tibble tidyselect utf8 vctrs viridisLite withr XVector zlibbioc

Subsampling single-cell data sets with sketchR

Rendered fromsketchR.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-02-23
Started: 2022-01-20

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Compare the compositions of a data set and a subset	compareCompositionPlot
Run geosketch to subsample a matrix	geosketch
Get names of geosketch functions	getGeosketchNames
Get names of scSampler functions	getScSamplerNames
Create diagnostic plot of Hausdorff distances	hausdorffDistPlot
Run scSampler to subsample a matrix	scsampler