Scale4C

DOI: 10.18129/B9.bioc.Scale4C    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see Scale4C.

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

Bioconductor version: 3.9

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.

Author: Carolin Walter

Maintainer: Carolin Walter <carolin.walter at uni-muenster.de>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Scale4C")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("Scale4C")

 

PDF	R Script	Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data
PDF		Reference Manual
Text		NEWS

Details

biocViews	Coverage, DataImport, QualityControl, Sequencing, Software, Visualization
Version	1.6.0
In Bioconductor since	BioC 3.6 (R-3.4) (2 years)
License	LGPL-3
Depends	R (>= 3.4), smoothie, GenomicRanges, IRanges, SummarizedExperiment
Imports	methods, grDevices, graphics, utils
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	Scale4C_1.6.0.tar.gz
Windows Binary	Scale4C_1.6.0.zip
Mac OS X 10.11 (El Capitan)	Scale4C_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Scale4C
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Scale4C
Package Short Url	https://bioconductor.org/packages/Scale4C/
Package Downloads Report	Download Stats