Package: Scale4C 1.35.0

Carolin Walter

Scale4C: Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data

Scale4C is an R/Bioconductor package for scale-space transformation and visualization of 4C-seq data. The scale-space transformation is a multi-scale visualization technique to transform a 2D signal (e.g. 4C-seq reads on a genomic interval of choice) into a tesselation in the scale space (2D, genomic position x scale factor) by applying different smoothing kernels (Gauss, with increasing sigma). This transformation allows for explorative analysis and comparisons of the data's structure with other samples.

Authors:Carolin Walter

Scale4C_1.35.0.tar.gz
Scale4C_1.35.0.zip(r-4.7)Scale4C_1.35.0.zip(r-4.6)Scale4C_1.35.0.zip(r-4.5)
Scale4C_1.35.0.tgz(r-4.6-any)Scale4C_1.35.0.tgz(r-4.5-any)
Scale4C_1.35.0.tar.gz(r-4.7-any)Scale4C_1.35.0.tar.gz(r-4.6-any)
Scale4C_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
Scale4C/json (API)
NEWS

# Install 'Scale4C' in R:
install.packages('Scale4C', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • liverData - Example 4C-seq data set of fetal liver data
  • liverDataVP - Example 4C-seq data set of fetal liver data, with added VP

On BioConductor:Scale4C-1.35.0(bioc 3.24)Scale4C-1.34.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

visualizationqualitycontroldataimportsequencingcoverage

3.48 score 6 scripts 438 downloads 22 exports 18 dependencies

Last updated from:c86a0613a4. Checks:1 ERROR, 9 OK. Indexed: yes.

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bioc-checksERROR168
linux-devel-x86_64OK252
source / vignettesOK209
linux-release-x86_64OK248
macos-release-arm64OK176
macos-oldrel-arm64OK149
windows-develOK207
windows-releaseOK188
windows-oldrelOK184
wasm-releaseOK111

Exports:addPointsOfInterestcalculateFingerprintMapcalculateScaleSpacefindSingularitiesimportBasic4CseqDataoutputScaleSpaceTreeplotInflectionPointsplotTesselationplotTracebackpointsOfInterestpointsOfInterest<-rawDatarawData<-Scale4CscaleSpacescaleSpace<-singularitiessingularities<-viewpointviewpoint<-viewpointChromosomeviewpointChromosome<-

Dependencies:abindBiobaseBiocGenericsDelayedArraygenericsGenomicRangesIRangeslatticeMatrixMatrixGenericsmatrixStatsS4ArraysS4VectorsSeqinfosmoothieSparseArraySummarizedExperimentXVector

Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data

Rendered fromvignette.Rnwusingutils::Sweaveon May 30 2026.

Last update: 2017-06-22
Started: 2017-06-22

Readme and manuals

Help Manual

Help pageTopics
Add points of interest to a 'Scale4C' objectaddPointsOfInterest addPointsOfInterest,Scale4C,data.frame-method
Calculate scale-space fingerprint map for given 4C-seq datacalculateFingerprintMap calculateFingerprintMap,Scale4C-method
Calculate scale-space representation for given 4C-seq datacalculateScaleSpace calculateScaleSpace,Scale4C-method
Find singularities in a provided scale-space fingerprint mapfindSingularities findSingularities,Scale4C-method
Import raw data from a provided Basic4Cseq output fileimportBasic4CseqData importBasic4CseqData,character,numeric,character,numeric-method
Example 4C-seq data set of fetal liver dataliverData
Example 4C-seq data set of fetal liver data, with added VPliverDataVP
Output list of all features for a given scale-space mapoutputScaleSpaceTree outputScaleSpaceTree,Scale4C-method
Draw a smoothed near-cis profile with marked inflection points for a 4C-seq signalplotInflectionPoints plotInflectionPoints,Scale4C,numeric-method
Draw the final scale space tesselationplotTesselation plotTesselation,Scale4C-method
Draw the traceback results for a list of singular points on a fingerprint mapplotTraceback plotTraceback,Scale4C-method
Creating a Scale4C objectScale4C Scale4C,numeric,character,GRanges-method
Class '"Scale4C"'pointsOfInterest pointsOfInterest,Scale4C-method pointsOfInterest<- pointsOfInterest<-,Scale4C,GRanges-method rawData rawData,Scale4C-method rawData<- rawData<-,Scale4C,GRanges-method Scale4C-class scaleSpace scaleSpace,Scale4C-method scaleSpace<- scaleSpace<-,Scale4C,SummarizedExperiment-method singularities singularities,Scale4C-method singularities<- singularities<-,Scale4C,GRanges-method viewpoint viewpoint,Scale4C-method viewpoint<- viewpoint<-,Scale4C,numeric-method viewpointChromosome viewpointChromosome,Scale4C-method viewpointChromosome<- viewpointChromosome<-,Scale4C,character-method