Package: Scale4C 1.29.0
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:
Scale4C_1.29.0.tar.gz
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Scale4C_1.29.0.tgz(r-4.4-any)Scale4C_1.29.0.tgz(r-4.3-any)
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Scale4C.pdf |Scale4C.html✨
Scale4C/json (API)
NEWS
| # Install 'Scale4C' in R: |
| install.packages('Scale4C', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- 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-1.29.0(bioc 3.21)Scale4C-1.28.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
visualizationqualitycontroldataimportsequencingcoverage
Last updated 2 months agofrom:c88a0faee5. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 20 2024 |
| R-4.5-win | OK | Nov 20 2024 |
| R-4.5-linux | OK | Nov 20 2024 |
| R-4.4-win | OK | Nov 20 2024 |
| R-4.4-mac | OK | Nov 20 2024 |
| R-4.3-win | OK | Nov 20 2024 |
| R-4.3-mac | OK | Nov 20 2024 |
Exports:addPointsOfInterestcalculateFingerprintMapcalculateScaleSpacefindSingularitiesimportBasic4CseqDataoutputScaleSpaceTreeplotInflectionPointsplotTesselationplotTracebackpointsOfInterestpointsOfInterest<-rawDatarawData<-Scale4CscaleSpacescaleSpace<-singularitiessingularities<-viewpointviewpoint<-viewpointChromosomeviewpointChromosome<-
Dependencies:abindaskpassBiobaseBiocGenericscrayoncurlDelayedArraygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6S4ArraysS4VectorssmoothieSparseArraySummarizedExperimentsysUCSC.utilsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add points of interest to a 'Scale4C' object | addPointsOfInterest addPointsOfInterest,Scale4C,data.frame-method |
| Calculate scale-space fingerprint map for given 4C-seq data | calculateFingerprintMap calculateFingerprintMap,Scale4C-method |
| Calculate scale-space representation for given 4C-seq data | calculateScaleSpace calculateScaleSpace,Scale4C-method |
| Find singularities in a provided scale-space fingerprint map | findSingularities findSingularities,Scale4C-method |
| Import raw data from a provided Basic4Cseq output file | importBasic4CseqData importBasic4CseqData,character,numeric,character,numeric-method |
| Example 4C-seq data set of fetal liver data | liverData |
| Example 4C-seq data set of fetal liver data, with added VP | liverDataVP |
| Output list of all features for a given scale-space map | outputScaleSpaceTree outputScaleSpaceTree,Scale4C-method |
| Draw a smoothed near-cis profile with marked inflection points for a 4C-seq signal | plotInflectionPoints plotInflectionPoints,Scale4C,numeric-method |
| Draw the final scale space tesselation | plotTesselation plotTesselation,Scale4C-method |
| Draw the traceback results for a list of singular points on a fingerprint map | plotTraceback plotTraceback,Scale4C-method |
| Creating a Scale4C object | Scale4C 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 |