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Scale4C

This is the development version of Scale4C; for the stable release version, see Scale4C.

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

Bioconductor version: Development (3.18)

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>

Citation (from within R, enter citation("Scale4C")):

Installation

To install this package, start R (version "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Coverage, DataImport, QualityControl, Sequencing, Software, Visualization
Version 1.23.0
In Bioconductor since BioC 3.6 (R-3.4) (6 years)
License LGPL-3
Depends R (>= 3.4), smoothie, GenomicRanges, IRanges, SummarizedExperiment
Imports methods, grDevices, graphics, utils
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Package Archives

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

Source Package Scale4C_1.23.0.tar.gz
Windows Binary Scale4C_1.23.0.zip (64-bit only)
macOS Binary (x86_64) Scale4C_1.23.0.tgz
macOS Binary (arm64) Scale4C_1.23.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/Scale4C
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Scale4C
Bioc Package Browser https://code.bioconductor.org/browse/Scale4C/
Package Short Url https://bioconductor.org/packages/Scale4C/
Package Downloads Report Download Stats