Package: swissknife 0.41

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'))

Peer review:

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

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

24 exports 8 stars 3.68 score 72 dependencies 10 scripts

Last updated 5 months agofrom:bbfe1f9020. Checks:OK: 1 NOTE: 3 ERROR: 5. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 16 2024
R-4.5-win-x86_64ERRORSep 16 2024
R-4.5-linux-x86_64NOTESep 16 2024
R-4.4-win-x86_64ERRORSep 16 2024
R-4.4-mac-x86_64NOTESep 16 2024
R-4.4-mac-aarch64NOTESep 16 2024
R-4.3-win-x86_64ERRORSep 16 2024
R-4.3-mac-x86_64ERRORSep 16 2024
R-4.3-mac-aarch64ERRORSep 16 2024

Exports:addUtilsFunctionsannotateRegionscalcAndCountDistcalcPhasogramcol2hexestimateNRLgetGenomicTilesgetInsertSizeDistFromBamgetMappableRegionslabelCellsloadExampleDatanormGenesetExpressionparsePkgVersionsplotBitScatterplotGeneRegionplotPhasogramplotSelVarGenesprepareGTFreadSampleTsvssampleControlElementsselVarGenesspecificityScorevalueToColorweightedMeanByID

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelclicliprcodetoolscpp11crayoncredentialscurlDelayedArraydescdplyrfansiformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgertghgitcredsgluehttrhttr2iniIRangesjsonliteKernSmoothlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigpngpurrrR6rappdirsRcpprlangrprojrootrstudioapiS4ArraysS4VectorssnowSparseArraySummarizedExperimentsystibbletidyselectUCSC.utilsusethisutf8vctrswhiskerwithrXVectoryamlzipzlibbioc

Readme and manuals

Help Manual

Help pageTopics
swissknife - handy code shared in the FMI CompBio groupswissknife-package swissknife
Copy utility functions to packageaddUtilsFunctions
Annotate regions.annotateRegions
Count frequency of differences between values in integer vectors.calcAndCountDist
Calculate phasograms (same strand alignment distances).calcPhasogram
Get hex colorcol2hex
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 geneslabelCells
Access example dataloadExampleData
Calculate normalized expression of a gene setnormGenesetExpression
Parse R and R package versions from session informationsparsePkgVersions
Create a bitmap-rendered plot.plotBitScatter
Plot gene regionplotGeneRegion
Plot annotated phasogram.plotPhasogram
Plot Selected Variable GenesplotSelVarGenes
Prepare GTF file for use with plotGeneRegionprepareGTF
Read sample tsv files from seqdata storagereadSampleTsvs
Sample control elements that match a target distribution.sampleControlElements
Select Variable Genes in Single Cell RNA-seqselVarGenes
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 meanweightedMeanByID