Package: swissknife 0.42

Michael Stadler

swissknife: Handy code shared in the FMI CompBio group

A collection of useful R functions performing various tasks that might be re-usable and worth sharing.

Authors:Michael Stadler [aut, cre], Charlotte Soneson [aut], Panagiotis Papasaikas [aut], Dania Machlab [aut], Fiona Ross [aut], Friedrich Miescher Institute for Biomedical Research [cph]

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swissknife.pdf |swissknife.html✨
swissknife/json (API)
NEWS

# Install 'swissknife' in R:

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

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

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

cpp

3.76 score 8 stars 12 scripts 24 exports 71 dependencies

Last updated 2 months agofrom:d1d2146b4a. Checks:1 OK, 6 ERROR, 5 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 07 2025
R-4.5-win-x86_64	ERROR	Mar 07 2025
R-4.5-mac-x86_64	NOTE	Mar 07 2025
R-4.5-mac-aarch64	NOTE	Mar 07 2025
R-4.5-linux-x86_64	ERROR	Mar 07 2025
R-4.4-win-x86_64	ERROR	Mar 07 2025
R-4.4-mac-x86_64	NOTE	Mar 07 2025
R-4.4-mac-aarch64	NOTE	Mar 07 2025
R-4.4-linux-x86_64	ERROR	Mar 07 2025
R-4.3-win-x86_64	ERROR	Mar 07 2025
R-4.3-mac-x86_64	NOTE	Mar 07 2025
R-4.3-mac-aarch64	ERROR	Mar 07 2025

Exports:addUtilsFunctions annotateRegions calcAndCountDist calcPhasogram col2hex estimateNRL getGenomicTiles getInsertSizeDistFromBam getMappableRegions labelCells loadExampleData normGenesetExpression parsePkgVersions plotBitScatter plotGeneRegion plotPhasogram plotSelVarGenes prepareGTF readSampleTsvs sampleControlElements selVarGenes specificityScore valueToColor weightedMeanByID

Dependencies:abind askpass BH Biobase BiocGenerics BiocParallel cli clipr codetools cpp11 crayon credentials curl DelayedArray desc dplyr fansi formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges gert gh gitcreds glue httr httr2 ini IRanges jsonlite KernSmooth lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats mime openssl pillar pkgconfig png purrr R6 rappdirs Rcpp rlang rprojroot rstudioapi S4Arrays S4Vectors snow SparseArray SummarizedExperiment sys tibble tidyselect UCSC.utils usethis utf8 vctrs whisker withr XVector yaml zip

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
swissknife - handy code shared in the FMI CompBio group	swissknife-package swissknife
Copy utility functions to package	addUtilsFunctions
Annotate regions.	annotateRegions
Count frequency of differences between values in integer vectors.	calcAndCountDist
Calculate phasograms (same strand alignment distances).	calcPhasogram
Get hex color	col2hex
Estimate the nucleosome repeat length (NRL) from a phasogram.	estimateNRL
Get regions tiling a genome.	getGenomicTiles
Tabulate insert sizes from paired-end alignments in bam files.	getInsertSizeDistFromBam
Get mappable regions of a genome.	getMappableRegions
Assign labels to cells using known marker genes	labelCells
Access example data	loadExampleData
Calculate normalized expression of a gene set	normGenesetExpression
Parse R and R package versions from session informations	parsePkgVersions
Create a bitmap-rendered plot.	plotBitScatter
Plot gene region	plotGeneRegion
Plot annotated phasogram.	plotPhasogram
Plot Selected Variable Genes	plotSelVarGenes
Prepare GTF file for use with plotGeneRegion	prepareGTF
Read sample tsv files from seqdata storage	readSampleTsvs
Sample control elements that match a target distribution.	sampleControlElements
Select Variable Genes in Single Cell RNA-seq	selVarGenes
Calculate gene-expression specificity scores.	specificityScore specificityScore,matrix-method specificityScore,SummarizedExperiment-method
Map numerical values to colors.	valueToColor
Aggregate different rows assigned to the same ID by calculating a weighted mean	weightedMeanByID