Welcome to the new bioconductor.org!

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 (3.19)

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 "4.4") 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 1.25.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License LGPL-3
Depends R (>= 3.4), smoothie, GenomicRanges, IRanges, SummarizedExperiment
Imports methods, grDevices, graphics, utils
System Requirements
URL
See More
Suggests
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package Scale4C_1.25.0.tar.gz
Windows Binary Scale4C_1.25.0.zip (64-bit only)
macOS Binary (x86_64) Scale4C_1.25.0.tgz
macOS Binary (arm64) Scale4C_1.25.0.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