Scale4C
This is the released version of Scale4C; for the devel version, see Scale4C.
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("Scale4C")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
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 |
See More
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Scale4C_1.34.0.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/Scale4C/ |
| Package Short Url | https://bioconductor.org/packages/Scale4C/ |
| Package Downloads Report | Download Stats |