Scale4C

This is the released version of Scale4C; for the devel version, see Scale4C.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6

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

Bioconductor version: Release (3.23)

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")):

Carolin Walter. Scale4C: Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data. doi:10.18129/B9.bioc.Scale4C, R package version 1.34.0, https://bioconductor.org/packages/Scale4C.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Coverage, DataImport, QualityControl, Sequencing, Software, Visualization
Version	1.34.0
In Bioconductor since	BioC 3.6 (R-3.4) (9 years)
License	LGPL-3
Depends	R (>= 3.5.0), smoothie, GenomicRanges, IRanges, SummarizedExperiment
Imports	methods, grDevices, graphics, utils
System Requirements
URL

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Build Report	Build Report, r-universe

Package Archives

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

Source Package	Scale4C_1.34.0.tar.gz
Windows Binary (x86_64)	Scale4C_1.34.0.zip
macOS Binary (big-sur-x86_64)	Scale4C_1.34.0.tgz
macOS Binary (sonoma-arm64)	Scale4C_1.34.0.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