Scale4C

DOI: 10.18129/B9.bioc.Scale4C    

This package is for version 3.13 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: 3.13

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 "4.1") 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	1.14.0
In Bioconductor since	BioC 3.6 (R-3.4) (4 years)
License	LGPL-3
Depends	R (>= 3.4), smoothie, GenomicRanges, IRanges, SummarizedExperiment
Imports	methods, grDevices, graphics, utils
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	Scale4C_1.14.0.tar.gz
Windows Binary	Scale4C_1.14.0.zip
macOS 10.13 (High Sierra)	Scale4C_1.14.0.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