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>
citation("Scale4C")):
Installation
To install this package, start R (version "3.6") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Coverage, DataImport, QualityControl, Sequencing, Software, Visualization |
| Version | 1.6.0 |
| 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 | |
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| Build Report | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/Scale4C/ |
| Package Short Url | https://bioconductor.org/packages/Scale4C/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |